17-58214788-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_017777.4(MKS1):c.468C>T(p.Val156=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000716 in 1,606,748 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). Synonymous variant affecting the same amino acid position (i.e. V156V) has been classified as Likely benign.
Frequency
Consequence
NM_017777.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MKS1 | NM_017777.4 | c.468C>T | p.Val156= | synonymous_variant | 5/18 | ENST00000393119.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MKS1 | ENST00000393119.7 | c.468C>T | p.Val156= | synonymous_variant | 5/18 | 1 | NM_017777.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152082Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000736 AC: 18AN: 244472Hom.: 0 AF XY: 0.0000827 AC XY: 11AN XY: 133068
GnomAD4 exome AF: 0.0000722 AC: 105AN: 1454666Hom.: 0 Cov.: 30 AF XY: 0.0000732 AC XY: 53AN XY: 723918
GnomAD4 genome AF: 0.0000658 AC: 10AN: 152082Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74292
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 09, 2018 | - - |
Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 10, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at