rs6427419
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018240.7(KIRREL1):c.917-8C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 1,608,044 control chromosomes in the GnomAD database, including 221,194 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_018240.7 splice_region, splice_polypyrimidine_tract, 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 |
---|---|---|---|---|---|---|---|
KIRREL1 | NM_018240.7 | c.917-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000359209.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIRREL1 | ENST00000359209.11 | c.917-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_018240.7 | P1 | |||
KIRREL1 | ENST00000360089.8 | c.425-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
KIRREL1 | ENST00000368172.2 | c.565-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
KIRREL1 | ENST00000368173.7 | c.617-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.421 AC: 63854AN: 151670Hom.: 16480 Cov.: 30
GnomAD3 exomes AF: 0.533 AC: 131791AN: 247138Hom.: 37591 AF XY: 0.536 AC XY: 71651AN XY: 133564
GnomAD4 exome AF: 0.523 AC: 762221AN: 1456252Hom.: 204697 Cov.: 51 AF XY: 0.525 AC XY: 380338AN XY: 724154
GnomAD4 genome ? AF: 0.421 AC: 63880AN: 151792Hom.: 16497 Cov.: 30 AF XY: 0.428 AC XY: 31770AN XY: 74174
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at