1:2338250-2338250 C > G

Classification

Category 4

curation

CMH MAF

61 / 14969 samples (0.408%)
59 het., 2 hom. (96.7%)
63 / 29938 total alleles (0.21%)

Genes

Consequences
gene: PEX10 synonym(s): NALD, PBD6A, PBD6B, RNF69, PEX10, ENSG00000157911

NM_002617.3 [CDS]
hgvs_c: NM_002617.3:c.685G>C
reference AA: V
variant AA: L
reference codon: Gtg
variant codon: Ctg
cDNA pos: 754
CDS pos: 685
translation impact: non_synonymous
protein sequence: NP_002608.1
AA pos: 229
hgvs_p: NP_002608.1:p.Val229Leu
blosum: 1
SIFT: tolerated (0.34)
PolyPhen2: benign (0.002)

NM_153818.1 [CDS] Reportable
hgvs_c: NM_153818.1:c.745G>C
reference AA: V
variant AA: L
reference codon: Gtg
variant codon: Ctg
cDNA pos: 814
CDS pos: 745
translation impact: non_synonymous
protein sequence: NP_722540.1
AA pos: 249
hgvs_p: NP_722540.1:p.Val249Leu
blosum: 1
SIFT: tolerated (0.34)
PolyPhen2: benign (0.001)

dbSNP

rs139345520
GMAF = 0.006589
TOPMED_MAF = 0.00661792813455657

ClinVar

296277
clinvar_significance = Conflicting_interpretations_of_pathogenicity
clinvar_disease = Peroxisome biogenesis disorder 1A (Zellweger)

Exome Variant Server

EVS
EVS MAF (European American/African American/All) = 0.000116,0.018207,0.006237

ExAC

ExAC
Ethnicity Count / Number MAF
African 183 / 7528 2.43%
America/Latino 6 / 8836 0.0679%
East Asian 0 / 7122 0%
Finnish 0 / 3500 0%
Non-Finnish 3 / 51760 0.0058%
Other 0 / 638 0%
South Asian 0 / 13724 0%
Total MAF 192 / 93108 0.206%

gnomAD

gnomAD
Source: Genome / Exome

Ethnicity Count / Number MAF
African 517 / 23864 2.17%
America/Latino 37 / 34822 0.106%
Ashkenazi Jewish 0 / 10134 0%
East Asian 0 / 19658 0%
Finnish 0 / 23954 0%
Non-Finnish 10 / 124976 0.008%
Other 7 / 6994 0.1%
South Asian 0 / 29958 0%
Korean 0 / 3784 0%
Japanese 0 / 122 0%
Other East Asian 0 / 14192 0%
Bulgarian 0 / 2414 0%
Estonian 0 / 4820 0%
North-Western European 4 / 50150 0.00798%
Southern European 2 / 11100 0.018%
Swedish 0 / 24972 0%
Other non-Finnish European 4 / 31520 0.0127%
Total MAF 571 / 274360 0.208%

curated_classification = 4

Export Variant

Curation

Likely Benign