11-62338024-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001083926.2(ASRGL1):c.47C>G(p.Ser16Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000809 in 1,607,846 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_001083926.2 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 |
---|---|---|---|---|---|---|---|---|
ASRGL1 | NM_001083926.2 | c.47C>G | p.Ser16Cys | missense_variant | Exon 2 of 7 | ENST00000415229.6 | NP_001077395.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152258Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000421 AC: 1AN: 237296Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 128760
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1455588Hom.: 0 Cov.: 32 AF XY: 0.00000276 AC XY: 2AN XY: 723534
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152258Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74380
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces serine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 16 of the ASRGL1 protein (p.Ser16Cys). This variant is present in population databases (rs752659253, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with ASRGL1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1503938). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at