chr5-169883181-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001129891.3(INSYN2B):c.718C>T(p.Arg240Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000973 in 1,551,484 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001129891.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INSYN2B | NM_001129891.3 | c.718C>T | p.Arg240Cys | missense_variant | 2/4 | ENST00000377365.4 | |
DOCK2 | NM_004946.3 | c.2799+42329G>A | intron_variant | ENST00000520908.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INSYN2B | ENST00000377365.4 | c.718C>T | p.Arg240Cys | missense_variant | 2/4 | 2 | NM_001129891.3 | P1 | |
DOCK2 | ENST00000520908.7 | c.2799+42329G>A | intron_variant | 2 | NM_004946.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000834 AC: 13AN: 155852Hom.: 0 AF XY: 0.0000727 AC XY: 6AN XY: 82534
GnomAD4 exome AF: 0.0000993 AC: 139AN: 1399342Hom.: 0 Cov.: 32 AF XY: 0.0000811 AC XY: 56AN XY: 690176
GnomAD4 genome ? AF: 0.0000789 AC: 12AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74324
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at