rs3115627
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000647952.1(ENSG00000290870):n.2156-15T>C variant causes a splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,216 control chromosomes in the GnomAD database, including 7,307 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
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 |
---|---|---|---|---|---|---|---|
LOC105375010 | XR_926681.2 | n.42-15T>C | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | ||||
LOC105375010 | XR_926680.3 | n.42-15T>C | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | ||||
LOC105375010 | XR_926682.3 | n.42-15T>C | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000647952.1 | n.2156-15T>C | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | |||||||
ENST00000432679.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.308 AC: 46763AN: 151842Hom.: 7283 Cov.: 32
GnomAD4 exome AF: 0.332 AC: 85AN: 256Hom.: 11 Cov.: 0 AF XY: 0.307 AC XY: 43AN XY: 140
GnomAD4 genome AF: 0.308 AC: 46792AN: 151960Hom.: 7296 Cov.: 32 AF XY: 0.305 AC XY: 22648AN XY: 74274
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at