1:40539750-40539750 T > C

Classification

Category 3

non_synonymous

CMH MAF

35 / 14969 samples (0.234%)
35 het., 0 hom. (100%)
35 / 29938 total alleles (0.117%)

Genes

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

TRNAN-GUU [intron] Reportable

gene: PPT1 synonym(s): CLN1, INCL, PPT, PPT1, ENSG00000131238

NM_000310.3 [CDS] Reportable
hgvs_c: NM_000310.3:c.904A>G
reference AA: I
variant AA: V
reference codon: Ata
variant codon: Gta
cDNA pos: 1136
CDS pos: 904
translation impact: non_synonymous
protein sequence: NP_000301.1
AA pos: 302
hgvs_p: NP_000301.1:p.Ile302Val
blosum: 3
SIFT: tolerated (0.32)
PolyPhen2: benign (0.016)

NM_001142604.1 [CDS]
hgvs_c: NM_001142604.1:c.595A>G
reference AA: I
variant AA: V
reference codon: Ata
variant codon: Gta
cDNA pos: 827
CDS pos: 595
translation impact: non_synonymous
protein sequence: NP_001136076.1
AA pos: 199
hgvs_p: NP_001136076.1:p.Ile199Val
blosum: 3
SIFT: tolerated (0.3)
PolyPhen2: benign (0.005)

dbSNP

rs146902902
GMAF = 0.0003994
TOPMED_MAF = 0.00081230886850152

ClinVar

199009
clinvar_significance = Uncertain_significance
clinvar_disease = Ceroid lipofuscinosis neuronal 1
clinvar_disease = History of neurodevelopmental disorder
clinvar_disease = Neuronal Ceroid-Lipofuscinosis

Exome Variant Server

EVS
EVS MAF (European American/African American/All) = 0.000698,0.000454,0.000615

ExAC

ExAC
Ethnicity Count / Number MAF
African 5 / 10406 0.048%
America/Latino 19 / 11578 0.164%
East Asian 0 / 8654 0%
Finnish 9 / 6612 0.136%
Non-Finnish 115 / 66730 0.172%
Other 0 / 908 0%
South Asian 11 / 16512 0.0666%
Total MAF 159 / 121400 0.131%

gnomAD

gnomAD
Source: Genome / Exome

Ethnicity Count / Number MAF
African 9 / 24968 0.036%
America/Latino 34 / 35438 0.0959%
Ashkenazi Jewish 0 / 10370 0%
East Asian 0 / 19954 0%
Finnish 24 / 25110 0.0956%
Non-Finnish 224 / 129132 0.173%
Other 9 / 7222 0.125%
South Asian 25 / 30616 0.0817%
Korean 0 / 3818 0%
Japanese 0 / 152 0%
Other East Asian 0 / 14424 0%
Bulgarian 8 / 2668 0.3%
Estonian 11 / 4830 0.228%
North-Western European 76 / 50780 0.15%
Southern European 8 / 11608 0.0689%
Swedish 73 / 26134 0.279%
Other non-Finnish European 48 / 33112 0.145%
Total MAF 325 / 282810 0.115%


Export Variant

Curation

Uncertain Significance