rs35986685
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002447.4(MST1R):āc.1838A>Cā(p.Gln613Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.011 in 1,614,098 control chromosomes in the GnomAD database, including 230 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002447.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MST1R | NM_002447.4 | c.1838A>C | p.Gln613Pro | missense_variant | 5/20 | ENST00000296474.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MST1R | ENST00000296474.8 | c.1838A>C | p.Gln613Pro | missense_variant | 5/20 | 1 | NM_002447.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00674 AC: 1025AN: 152168Hom.: 13 Cov.: 33
GnomAD3 exomes AF: 0.0110 AC: 2758AN: 251404Hom.: 40 AF XY: 0.0134 AC XY: 1819AN XY: 135894
GnomAD4 exome AF: 0.0115 AC: 16787AN: 1461812Hom.: 217 Cov.: 32 AF XY: 0.0128 AC XY: 9316AN XY: 727204
GnomAD4 genome AF: 0.00671 AC: 1022AN: 152286Hom.: 13 Cov.: 33 AF XY: 0.00725 AC XY: 540AN XY: 74462
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 15, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at