rs1009948
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_001564.2(XIST):n.11437-464G>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 0.0932 in 112,963 control chromosomes in the GnomAD database, including 615 homozygotes. There are 2,871 hemizygotes in GnomAD. 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
Consequence
NR_001564.2 intron, non_coding_transcript
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XIST | NR_001564.2 | n.11437-464G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XIST | ENST00000429829.6 | n.11407-464G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0936 AC: 10390AN: 110985Hom.: 611 Cov.: 22 AF XY: 0.0853 AC XY: 2834AN XY: 33223
GnomAD4 exome AF: 0.0681 AC: 131AN: 1925Hom.: 4 AF XY: 0.256 AC XY: 32AN XY: 125
GnomAD4 genome ? AF: 0.0936 AC: 10393AN: 111038Hom.: 611 Cov.: 22 AF XY: 0.0853 AC XY: 2839AN XY: 33286
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at