11-3641832-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_053017.5(ART5):c.31G>T(p.Gly11Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000507 in 1,578,540 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_053017.5 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 |
---|---|---|---|---|---|---|---|
ART5 | NM_053017.5 | c.31G>T | p.Gly11Cys | missense_variant | 1/4 | ENST00000397068.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ART5 | ENST00000397068.8 | c.31G>T | p.Gly11Cys | missense_variant | 1/4 | 1 | NM_053017.5 | P1 | |
ART5 | ENST00000359918.8 | c.31G>T | p.Gly11Cys | missense_variant | 2/5 | 1 | P1 | ||
ART5 | ENST00000397067.7 | c.31G>T | p.Gly11Cys | missense_variant | 1/4 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000262 AC: 50AN: 190558Hom.: 0 AF XY: 0.000255 AC XY: 26AN XY: 101894
GnomAD4 exome AF: 0.000536 AC: 764AN: 1426418Hom.: 1 Cov.: 60 AF XY: 0.000507 AC XY: 358AN XY: 705918
GnomAD4 genome AF: 0.000243 AC: 37AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.000256 AC XY: 19AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2023 | The c.31G>T (p.G11C) alteration is located in exon 1 (coding exon 1) of the ART5 gene. This alteration results from a G to T substitution at nucleotide position 31, causing the glycine (G) at amino acid position 11 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