1:22161394-22161394 C > T

Classification

Category 4 curation
CMH MAF 132 / 14969 samples (0.882%)
131 het., 1 hom. (99.2%)
133 / 29938 total alleles (0.444%)

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

TRNAN-GUU [intron]

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

OMIM
OMIM:142461: HSPG2 (Autosomal recessive inheritance)
OMIM:224410: Dyssegmental dysplasia, Silverman-Handmaker type
OMIM:255800: Schwartz-Jampel syndrome, type 1

NM_005529.5 [CDS]
hgvs_c: NM_005529.5:c.10498G>A
reference AA: V
variant AA: M
reference codon: Gtg
variant codon: Atg
cDNA pos: 10538
CDS pos: 10498
translation impact: non_synonymous
protein sequence: NP_005520.4
AA pos: 3500
hgvs_p: NP_005520.4:p.Val3500Met
blosum: 1
PolyPhen2: probably_damaging (0.98)

rs143543800
GMAF = 0.001597
TOPMED_MAF = 0.00344036697247706

198669
clinvar_significance = Benign

EVS
EVS MAF (European American/African American/All) = 0.004070,0.000908,0.002999

ExAC America/Latino, (109 / 11556), 0.943%
COSMIC Mutation ID = COSV65933271
COSMIC_FATHMM_PREDICTION = PATHOGENIC
COSMIC_MUTATION_SOMATIC_STATUS = true

gnomAD Ashkenazi Jewish, (229 / 10356), 2.21% curated_classification = 4