chr3-49890070-G-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_002447.4(MST1R):c.3811-10C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0755 in 1,589,556 control chromosomes in the GnomAD database, including 4,798 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_002447.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0741 AC: 11279AN: 152154Hom.: 444 Cov.: 32
GnomAD3 exomes AF: 0.0625 AC: 14276AN: 228480Hom.: 489 AF XY: 0.0629 AC XY: 7693AN XY: 122380
GnomAD4 exome AF: 0.0756 AC: 108701AN: 1437284Hom.: 4354 Cov.: 32 AF XY: 0.0747 AC XY: 53208AN XY: 712376
GnomAD4 genome AF: 0.0741 AC: 11285AN: 152272Hom.: 444 Cov.: 32 AF XY: 0.0718 AC XY: 5350AN XY: 74466
ClinVar
Submissions by phenotype
MST1R-related disorder Benign:1
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