1:22161190-22161190 C > T

Classification

Category 4

curation

CMH MAF

91 / 14969 samples (0.608%)
90 het., 1 hom. (98.9%)
92 / 29938 total alleles (0.307%)

Genes

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

TRNAN-GUU [intron] Reportable

gene: HSPG2 synonym(s): HSPG, PLC, PRCAN, SJA, SJS, SJS1, HSPG2, ENSG00000142798

NM_005529.5 [CDS] Reportable
hgvs_c: NM_005529.5:c.10702G>A
reference AA: V
variant AA: I
reference codon: Gtc
variant codon: Atc
cDNA pos: 10742
CDS pos: 10702
translation impact: non_synonymous
protein sequence: NP_005520.4
AA pos: 3568
hgvs_p: NP_005520.4:p.Val3568Ile
blosum: 3
PolyPhen2: probably_damaging (0.999)

dbSNP

rs115616224
GMAF = 0.008986
TOPMED_MAF = 0.00989105504587155

ClinVar

446053
clinvar_significance = Benign_Likely_benign

Exome Variant Server

EVS
EVS MAF (European American/African American/All) = 0.000465,0.029732,0.010380

ExAC

ExAC
Ethnicity Count / Number MAF
African 275 / 10362 2.65%
America/Latino 18 / 11548 0.156%
East Asian 0 / 8630 0%
Finnish 0 / 6602 0%
Non-Finnish 39 / 66496 0.0587%
Other 2 / 898 0.223%
South Asian 0 / 16506 0%
Total MAF 334 / 121042 0.276%

COSMIC

COSMIC Mutation ID = COSV65933142
COSMIC_FATHMM_PREDICTION = PATHOGENIC
COSMIC_MUTATION_SOMATIC_STATUS = true

gnomAD

gnomAD
Source: Genome / Exome

Ethnicity Count / Number MAF
African 692 / 24964 2.77%
America/Latino 56 / 35440 0.158%
Ashkenazi Jewish 41 / 10366 0.396%
East Asian 1 / 19946 0.00501%
Finnish 0 / 25120 0%
Non-Finnish 46 / 128942 0.0357%
Other 12 / 7222 0.166%
South Asian 1 / 30616 0.00327%
Korean 0 / 3818 0%
Japanese 0 / 152 0%
Other East Asian 1 / 14418 0.00694%
Bulgarian 1 / 2666 0.0375%
Estonian 0 / 4828 0%
North-Western European 10 / 50634 0.0197%
Southern European 16 / 11600 0.138%
Swedish 2 / 26130 0.00765%
Other non-Finnish European 17 / 33084 0.0514%
Total MAF 849 / 282616 0.3%

curated_classification = 4

Export Variant

Curation

Likely Benign