rs199910690
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017777.4(MKS1):c.1601G>A(p.Arg534Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000663 in 1,613,714 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_017777.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 151950Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000225 AC: 56AN: 248576Hom.: 0 AF XY: 0.000215 AC XY: 29AN XY: 134998
GnomAD4 exome AF: 0.0000582 AC: 85AN: 1461646Hom.: 0 Cov.: 32 AF XY: 0.0000550 AC XY: 40AN XY: 727120
GnomAD4 genome AF: 0.000145 AC: 22AN: 152068Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74334
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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This variant is associated with the following publications: (PMID: 24608809) -
Bardet-Biedl syndrome 13 Pathogenic:1
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not specified Uncertain:1
Variant summary: MKS1 c.1601G>A (p.Arg534Gln) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00023 in 248576 control chromosomes, predominantly at a frequency of 0.003 within the East Asian subpopulation in the gnomAD database. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 2.7 fold of the estimated maximal expected allele frequency for a pathogenic variant in MKS1 causing Meckel Syndrome Type 1 phenotype (0.0011), strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. c.1601G>A has been reported in the literature as a compound heterozygous genotype in at-least two comprehensively genotyped individuals with features of Bardet-Biedl syndrome (BBS) or a reported diagnosis of Joubert Syndrome 28;Bardet-Biedl Syndrome 13 (example, Xing_2014, Sun_2018) and as a non-informative genotype in one individual among of cohort of individuals with microcephaly analyzed by whole exome sequencing (example, Lee_2020). These data indicate that the variant may be associated with disease but do not provide unequivocal conclusions about the association of this variant with Meckel Syndrome Type 1 phenotype. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (VUS, n=1; likely benign, n=3). Based on the evidence outlined above, the variant was classified as VUS-possibly benign. -
Microcephaly Uncertain:1
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Bardet-Biedl syndrome 13;C3714506:Meckel syndrome, type 1;C4310705:Joubert syndrome 28 Uncertain:1
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Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis Benign:1
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Meckel syndrome, type 1 Benign:1
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MKS1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at