rs28382742
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001167.4(XIAP):c.*803G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001167.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XIAP | ENST00000371199.8 | c.*803G>T | 3_prime_UTR_variant | Exon 7 of 7 | 1 | NM_001167.4 | ENSP00000360242.3 | |||
XIAP | ENST00000355640.3 | c.*803G>T | 3_prime_UTR_variant | Exon 7 of 7 | 5 | ENSP00000347858.3 | ||||
XIAP | ENST00000422098.6 | c.*803G>T | 3_prime_UTR_variant | Exon 9 of 9 | 4 | ENSP00000405529.2 |
Frequencies
GnomAD3 genomes AF: 0.172 AC: 18263AN: 106197Hom.: 1442 Cov.: 20 AF XY: 0.131 AC XY: 3843AN XY: 29365
GnomAD3 exomes AF: 0.237 AC: 20842AN: 88057Hom.: 1809 AF XY: 0.242 AC XY: 7495AN XY: 30911
GnomAD4 exome AF: 0.211 AC: 52911AN: 250214Hom.: 3898 Cov.: 0 AF XY: 0.234 AC XY: 21810AN XY: 93330
GnomAD4 genome AF: 0.172 AC: 18259AN: 106228Hom.: 1440 Cov.: 20 AF XY: 0.131 AC XY: 3849AN XY: 29412
ClinVar
Submissions by phenotype
not provided Benign:1
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X-linked lymphoproliferative disease due to XIAP deficiency Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at