rs1062633
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002447.4(MST1R):c.4003A>G(p.Arg1335Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 1,613,852 control chromosomes in the GnomAD database, including 193,380 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). 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 -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MST1R | NM_002447.4 | c.4003A>G | p.Arg1335Gly | missense_variant | 20/20 | ENST00000296474.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MST1R | ENST00000296474.8 | c.4003A>G | p.Arg1335Gly | missense_variant | 20/20 | 1 | NM_002447.4 | P2 | |
MST1R | ENST00000621387.4 | c.3685A>G | p.Arg1229Gly | missense_variant | 18/18 | 1 | |||
MST1R | ENST00000344206.8 | c.3856A>G | p.Arg1286Gly | missense_variant | 19/19 | 5 | A2 | ||
MST1R | ENST00000411578.6 | c.*825A>G | 3_prime_UTR_variant, NMD_transcript_variant | 19/19 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.508 AC: 77240AN: 151986Hom.: 21084 Cov.: 33
GnomAD3 exomes AF: 0.408 AC: 102561AN: 251134Hom.: 23564 AF XY: 0.405 AC XY: 54987AN XY: 135768
GnomAD4 exome AF: 0.475 AC: 694059AN: 1461748Hom.: 172265 Cov.: 55 AF XY: 0.468 AC XY: 340628AN XY: 727178
GnomAD4 genome ? AF: 0.508 AC: 77320AN: 152104Hom.: 21115 Cov.: 33 AF XY: 0.493 AC XY: 36679AN XY: 74360
ClinVar
Submissions by phenotype
MST1R-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | This variant is classified as 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