chr5-161294271-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_001371727.1(GABRB2):c.1349G>A(p.Ser450Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000901 in 1,614,032 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001371727.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GABRB2 | NM_001371727.1 | c.1349G>A | p.Ser450Asn | missense_variant | Exon 10 of 10 | ENST00000393959.6 | NP_001358656.1 | |
GABRB2 | NM_021911.3 | c.1349G>A | p.Ser450Asn | missense_variant | Exon 11 of 11 | NP_068711.1 | ||
GABRB2 | NM_000813.3 | c.1235G>A | p.Ser412Asn | missense_variant | Exon 10 of 10 | NP_000804.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000473 AC: 72AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000497 AC: 125AN: 251324Hom.: 0 AF XY: 0.000486 AC XY: 66AN XY: 135816
GnomAD4 exome AF: 0.000945 AC: 1382AN: 1461846Hom.: 1 Cov.: 30 AF XY: 0.000861 AC XY: 626AN XY: 727224
GnomAD4 genome AF: 0.000473 AC: 72AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.000525 AC XY: 39AN XY: 74334
ClinVar
Submissions by phenotype
not provided Benign:2
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GABRB2: BS2 -
Inborn genetic diseases Benign:1
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. -
Intellectual disability Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at