rs6427130
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002995.3(XCL1):c.176+7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 1,603,556 control chromosomes in the GnomAD database, including 207,970 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002995.3 splice_region, intron
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 |
---|---|---|---|---|---|---|---|
XCL1 | NM_002995.3 | c.176+7C>T | splice_region_variant, intron_variant | ENST00000367818.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XCL1 | ENST00000367818.4 | c.176+7C>T | splice_region_variant, intron_variant | 1 | NM_002995.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.513 AC: 77272AN: 150566Hom.: 19795 Cov.: 32
GnomAD3 exomes AF: 0.467 AC: 116313AN: 249168Hom.: 27323 AF XY: 0.469 AC XY: 63143AN XY: 134644
GnomAD4 exome AF: 0.517 AC: 751770AN: 1452868Hom.: 188142 Cov.: 42 AF XY: 0.514 AC XY: 371526AN XY: 722716
GnomAD4 genome ? AF: 0.513 AC: 77343AN: 150688Hom.: 19828 Cov.: 32 AF XY: 0.509 AC XY: 37444AN XY: 73592
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at