chr11-101891434-A-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_178127.5(ANGPTL5):c.1012T>A(p.Cys338Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000341 in 1,613,828 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C338Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_178127.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANGPTL5 | NM_178127.5 | c.1012T>A | p.Cys338Ser | missense_variant | 9/9 | ENST00000334289.7 | |
ANGPTL5 | XM_011542735.4 | c.817T>A | p.Cys273Ser | missense_variant | 7/7 | ||
ANGPTL5 | XM_017017466.3 | c.592T>A | p.Cys198Ser | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANGPTL5 | ENST00000334289.7 | c.1012T>A | p.Cys338Ser | missense_variant | 9/9 | 1 | NM_178127.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 151994Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251454Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135902
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1461834Hom.: 1 Cov.: 31 AF XY: 0.0000495 AC XY: 36AN XY: 727216
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 151994Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74232
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 22, 2024 | The c.1012T>A (p.C338S) alteration is located in exon 9 (coding exon 8) of the ANGPTL5 gene. This alteration results from a T to A substitution at nucleotide position 1012, causing the cysteine (C) at amino acid position 338 to be replaced by a serine (S). 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