1:21903947-21903947 G > A

Classification

Category 4

curation

CMH MAF

72 / 14969 samples (0.481%)
72 het., 0 hom. (100%)
72 / 29938 total alleles (0.24%)

Genes

Consequences
gene: TRNAN-GUU synonym(s): TRNAN-GUU

TRNAN-GUU [intron] Reportable

gene: ALPL synonym(s): AP-TNAP, APTNAP, HOPS, TNAP, TNSALP, ALPL, ENSG00000162551

ENST00000374840.3 [CDS] Reportable
hgvs_c: ENST00000374840.3:c.1381G>A
reference AA: V
variant AA: I
reference codon: Gtc
variant codon: Atc
cDNA pos: 1631
CDS pos: 1381
translation impact: non_synonymous
protein sequence: ENSP00000363973.3
AA pos: 461
hgvs_p: ENSP00000363973.3:p.Val461Ile
blosum: 3
SIFT: tolerated (0.94)
PolyPhen2: benign (0.055)

ENST00000539907.1 [CDS]
hgvs_c: ENST00000539907.1:c.1150G>A
reference AA: V
variant AA: I
reference codon: Gtc
variant codon: Atc
cDNA pos: 1357
CDS pos: 1150
translation impact: non_synonymous
protein sequence: ENSP00000437674.1
AA pos: 384
hgvs_p: ENSP00000437674.1:p.Val384Ile
blosum: 3
SIFT: tolerated (0.86)
PolyPhen2: benign (0.056)

ENST00000540617.1 [CDS]
hgvs_c: ENST00000540617.1:c.1216G>A
reference AA: V
variant AA: I
reference codon: Gtc
variant codon: Atc
cDNA pos: 1473
CDS pos: 1216
translation impact: non_synonymous
protein sequence: ENSP00000442672.1
AA pos: 406
hgvs_p: ENSP00000442672.1:p.Val406Ile
blosum: 3
SIFT: tolerated (0.82)
PolyPhen2: benign (0.055)

dbSNP

rs34810399
GMAF = 0.007188
TOPMED_MAF = 0.00827440112130479

ClinVar

295552
clinvar_significance = Benign_Likely_benign
clinvar_disease = Hypophosphatasia

Exome Variant Server

EVS
EVS MAF (European American/African American/All) = 0.000233,0.022480,0.007774

ExAC

ExAC
Ethnicity Count / Number MAF
African 246 / 9486 2.59%
America/Latino 10 / 11434 0.0875%
East Asian 0 / 8458 0%
Finnish 0 / 6592 0%
Non-Finnish 6 / 63938 0.00938%
Other 4 / 866 0.462%
South Asian 4 / 16318 0.0245%
Total MAF 270 / 117092 0.231%

gnomAD

gnomAD
Source: Genome / Exome

Ethnicity Count / Number MAF
African 688 / 24412 2.82%
America/Latino 39 / 35294 0.111%
Ashkenazi Jewish 0 / 10278 0%
East Asian 0 / 19516 0%
Finnish 1 / 23076 0.00433%
Non-Finnish 12 / 125864 0.00953%
Other 10 / 7140 0.14%
South Asian 9 / 30490 0.0295%
Korean 0 / 3818 0%
Japanese 0 / 114 0%
Other East Asian 0 / 14024 0%
Bulgarian 0 / 2518 0%
Estonian 0 / 4792 0%
North-Western European 3 / 48944 0.00613%
Southern European 2 / 11402 0.0175%
Swedish 1 / 26070 0.00384%
Other non-Finnish European 6 / 32138 0.0187%
Total MAF 759 / 276070 0.275%

curated_classification = 4

Export Variant

Curation

Likely Benign