chr12-107319296-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001018072.2(ABTB3):c.356C>T(p.Ala119Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000719 in 1,390,716 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_001018072.2 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 |
---|---|---|---|---|---|---|---|
ABTB3 | NM_001018072.2 | c.356C>T | p.Ala119Val | missense_variant | 1/17 | ENST00000280758.10 | |
ABTB3 | NM_001347943.2 | c.356C>T | p.Ala119Val | missense_variant | 1/15 | ||
ABTB3 | XM_047428301.1 | c.356C>T | p.Ala119Val | missense_variant | 1/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABTB3 | ENST00000280758.10 | c.356C>T | p.Ala119Val | missense_variant | 1/17 | 5 | NM_001018072.2 | ||
ABTB3 | ENST00000490090.6 | c.356C>T | p.Ala119Val | missense_variant | 1/15 | 2 | |||
ABTB3 | ENST00000420571.6 | c.356C>T | p.Ala119Val | missense_variant | 1/15 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000727 AC: 1AN: 137548Hom.: 0 AF XY: 0.0000133 AC XY: 1AN XY: 75470
GnomAD4 exome AF: 7.19e-7 AC: 1AN: 1390716Hom.: 0 Cov.: 33 AF XY: 0.00000146 AC XY: 1AN XY: 686512
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 08, 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