3-58274720-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001320126.2(ABHD6):c.586G>A(p.Ala196Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,614,070 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001320126.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABHD6 | NM_001320126.2 | c.586G>A | p.Ala196Thr | missense_variant | 7/10 | ENST00000478253.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABHD6 | ENST00000478253.6 | c.586G>A | p.Ala196Thr | missense_variant | 7/10 | 2 | NM_001320126.2 | P1 | |
ABHD6 | ENST00000295962.8 | c.586G>A | p.Ala196Thr | missense_variant | 6/9 | 1 | P1 | ||
ABHD6 | ENST00000463756.5 | c.586G>A | p.Ala196Thr | missense_variant | 7/7 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251222Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135790
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727244
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | The c.586G>A (p.A196T) alteration is located in exon 6 (coding exon 5) of the ABHD6 gene. This alteration results from a G to A substitution at nucleotide position 586, causing the alanine (A) at amino acid position 196 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at