19-10093854-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_031917.3(ANGPTL6):c.790C>T(p.Arg264Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000251 in 1,610,612 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.790C>T | p.Arg264Cys | missense_variant | 4/6 | ENST00000253109.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANGPTL6 | ENST00000253109.5 | c.790C>T | p.Arg264Cys | missense_variant | 4/6 | 1 | NM_031917.3 | P1 | |
ANGPTL6 | ENST00000592641.5 | c.790C>T | p.Arg264Cys | missense_variant | 4/6 | 1 | P1 | ||
ANGPTL6 | ENST00000589181.5 | c.790C>T | p.Arg264Cys | missense_variant | 3/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000214 AC: 53AN: 248066Hom.: 0 AF XY: 0.000276 AC XY: 37AN XY: 134300
GnomAD4 exome AF: 0.000259 AC: 377AN: 1458266Hom.: 1 Cov.: 31 AF XY: 0.000274 AC XY: 199AN XY: 725580
GnomAD4 genome AF: 0.000184 AC: 28AN: 152346Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.790C>T (p.R264C) alteration is located in exon 4 (coding exon 3) of the ANGPTL6 gene. This alteration results from a C to T substitution at nucleotide position 790, causing the arginine (R) at amino acid position 264 to be replaced by a cysteine (C). 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