1-211946686-T-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_015434.4(INTS7):āc.2336A>Gā(p.Asn779Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000456 in 1,613,182 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_015434.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000322 AC: 49AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000537 AC: 135AN: 251208Hom.: 2 AF XY: 0.000618 AC XY: 84AN XY: 135826
GnomAD4 exome AF: 0.000470 AC: 687AN: 1460890Hom.: 3 Cov.: 29 AF XY: 0.000531 AC XY: 386AN XY: 726804
GnomAD4 genome AF: 0.000322 AC: 49AN: 152292Hom.: 0 Cov.: 33 AF XY: 0.000269 AC XY: 20AN XY: 74474
ClinVar
Submissions by phenotype
INTS7-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 01, 2022 | This variant is classified as likely 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