1:978974-978974 G > A

Classification

Category 4

curation

CMH MAF

121 / 13144 samples (0.921%)
119 het., 2 hom. (98.3%)
123 / 26288 total alleles (0.468%)

Genes

Consequences
gene: AGRN synonym(s): AGRN, ENSG00000188157

NM_198576.3 [CDS] Reportable
hgvs_c: NM_198576.3:c.1660G>A
reference AA: V
variant AA: M
reference codon: Gtg
variant codon: Atg
cDNA pos: 1710
CDS pos: 1660
translation impact: non_synonymous
protein sequence: NP_940978.2
AA pos: 554
hgvs_p: NP_940978.2:p.Val554Met
blosum: 1
SIFT: deleterious (0.0)
PolyPhen2: possibly_damaging (0.867)

dbSNP

rs79016973
GMAF = 0.01138
TOPMED_MAF = 0.00599675076452599

ClinVar

263165
clinvar_significance = Benign_Likely_benign
clinvar_disease = Myasthenic syndrome

Exome Variant Server

EVS
EVS MAF (European American/African American/All) = 0.004304,0.000454,0.003000

ExAC

ExAC
Ethnicity Count / Number MAF
African 7 / 9628 0.0727%
America/Latino 9 / 11350 0.0793%
East Asian 281 / 8404 3.34%
Finnish 193 / 6514 2.96%
Non-Finnish 491 / 63930 0.768%
Other 17 / 860 1.98%
South Asian 36 / 16348 0.22%
Total MAF 1034 / 117034 0.884%

COSMIC

COSMIC Mutation ID = COSV65069756
COSMIC_FATHMM_PREDICTION = PATHOGENIC
COSMIC_MUTATION_SOMATIC_STATUS = true

gnomAD

gnomAD
Source: Genome / Exome

Ethnicity Count / Number MAF
African 18 / 24454 0.0736%
America/Latino 39 / 35278 0.111%
Ashkenazi Jewish 15 / 10114 0.148%
East Asian 649 / 19768 3.28%
Finnish 520 / 19508 2.67%
Non-Finnish 869 / 123162 0.706%
Other 72 / 7026 1.02%
South Asian 74 / 30500 0.243%
Korean 71 / 3816 1.86%
Japanese 4 / 118 3.39%
Other East Asian 530 / 14274 3.71%
Bulgarian 31 / 2618 1.18%
Estonian 105 / 4790 2.19%
North-Western European 226 / 47522 0.476%
Southern European 58 / 11274 0.514%
Swedish 256 / 25970 0.986%
Other non-Finnish European 193 / 30988 0.623%
Total MAF 2256 / 269810 0.836%

curated_classification = 4

Export Variant

Curation

Likely Benign