17-58206021-C-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001321269.2(MKS1):āc.1655G>Cā(p.Ser552Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000271 in 1,562,064 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/5 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001321269.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00152 AC: 232AN: 152144Hom.: 2 Cov.: 32
GnomAD4 exome AF: 0.000136 AC: 192AN: 1409802Hom.: 0 Cov.: 32 AF XY: 0.000113 AC XY: 79AN XY: 696894
GnomAD4 genome AF: 0.00152 AC: 232AN: 152262Hom.: 2 Cov.: 32 AF XY: 0.00173 AC XY: 129AN XY: 74458
ClinVar
Submissions by phenotype
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