rs2274160
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015404.4(WHRN):c.1627-12G>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000696 in 1,436,838 control chromosomes in the GnomAD database, with no homozygous occurrence. 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
NM_015404.4 splice_polypyrimidine_tract, intron
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 |
---|---|---|---|---|---|---|---|
WHRN | NM_015404.4 | c.1627-12G>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000362057.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WHRN | ENST00000362057.4 | c.1627-12G>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_015404.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152006Hom.: 0 Cov.: 33 FAILED QC
GnomAD4 exome AF: 6.96e-7 AC: 1AN: 1436838Hom.: 0 Cov.: 32 AF XY: 0.00000140 AC XY: 1AN XY: 712494
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152006Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74228
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at