19-10092686-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_031917.3(ANGPTL6):c.1316G>A(p.Arg439Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000743 in 1,614,016 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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 Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANGPTL6 | NM_031917.3 | c.1316G>A | p.Arg439Gln | missense_variant | Exon 6 of 6 | ENST00000253109.5 | NP_114123.2 | |
SHFL | NM_018381.4 | c.*384C>T | 3_prime_UTR_variant | Exon 8 of 8 | ENST00000253110.16 | NP_060851.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANGPTL6 | ENST00000253109.5 | c.1316G>A | p.Arg439Gln | missense_variant | Exon 6 of 6 | 1 | NM_031917.3 | ENSP00000253109.3 | ||
SHFL | ENST00000253110.16 | c.*384C>T | 3_prime_UTR_variant | Exon 8 of 8 | 2 | NM_018381.4 | ENSP00000253110.10 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 248992Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134796
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461726Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727150
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1316G>A (p.R439Q) alteration is located in exon 6 (coding exon 5) of the ANGPTL6 gene. This alteration results from a G to A substitution at nucleotide position 1316, causing the arginine (R) at amino acid position 439 to be replaced by a glutamine (Q). 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