rs9266722
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000425174.1(HLA-S):n.49-67G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 352,166 control chromosomes in the GnomAD database, including 4,839 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.14 ( 1824 hom., cov: 31)
Exomes 𝑓: 0.16 ( 3015 hom. )
Consequence
HLA-S
ENST00000425174.1 intron, non_coding_transcript
ENST00000425174.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.333
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLA-S | ENST00000425174.1 | n.49-67G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.144 AC: 21857AN: 151912Hom.: 1821 Cov.: 31
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GnomAD4 exome AF: 0.162 AC: 32464AN: 200136Hom.: 3015 Cov.: 0 AF XY: 0.161 AC XY: 18338AN XY: 114124
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GnomAD4 genome ? AF: 0.144 AC: 21877AN: 152030Hom.: 1824 Cov.: 31 AF XY: 0.149 AC XY: 11097AN XY: 74330
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at