19-10093606-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_031917.3(ANGPTL6):c.965G>A(p.Arg322Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,613,382 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_031917.3 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 |
---|---|---|---|---|---|---|---|
ANGPTL6 | NM_031917.3 | c.965G>A | p.Arg322Gln | missense_variant | 5/6 | ENST00000253109.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANGPTL6 | ENST00000253109.5 | c.965G>A | p.Arg322Gln | missense_variant | 5/6 | 1 | NM_031917.3 | P1 | |
ANGPTL6 | ENST00000592641.5 | c.965G>A | p.Arg322Gln | missense_variant | 5/6 | 1 | P1 | ||
ANGPTL6 | ENST00000589181.5 | c.845G>A | p.Arg282Gln | missense_variant | 4/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000360 AC: 9AN: 249728Hom.: 0 AF XY: 0.0000518 AC XY: 7AN XY: 135082
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461146Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 726782
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74384
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 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