7-105542547-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_021930.6(RINT1):c.413C>T(p.Ala138Val) variant causes a missense change. The variant allele was found at a frequency of 0.00078 in 1,614,134 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A138T) has been classified as Likely benign.
Frequency
Consequence
NM_021930.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000618 AC: 94AN: 152136Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000465 AC: 117AN: 251482Hom.: 0 AF XY: 0.000441 AC XY: 60AN XY: 135918
GnomAD4 exome AF: 0.000797 AC: 1165AN: 1461880Hom.: 0 Cov.: 31 AF XY: 0.000785 AC XY: 571AN XY: 727246
GnomAD4 genome AF: 0.000617 AC: 94AN: 152254Hom.: 1 Cov.: 32 AF XY: 0.000524 AC XY: 39AN XY: 74462
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 02, 2020 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 23, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at