rs2304973
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001386809.1(CXCL16):c.80-7C>T 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 0.087 in 1,612,952 control chromosomes in the GnomAD database, including 7,133 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_001386809.1 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 |
---|---|---|---|---|---|---|---|
CXCL16 | NM_001386809.1 | c.80-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000293778.12 | |||
CXCL16 | NM_001100812.2 | c.80-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCL16 | ENST00000293778.12 | c.80-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001386809.1 | P1 | |||
CXCL16 | ENST00000574412.6 | c.80-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 | ||||
CXCL16 | ENST00000573123.1 | c.-90C>T | 5_prime_UTR_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0764 AC: 11598AN: 151800Hom.: 527 Cov.: 30
GnomAD3 exomes AF: 0.0989 AC: 24768AN: 250372Hom.: 1481 AF XY: 0.105 AC XY: 14257AN XY: 135338
GnomAD4 exome AF: 0.0881 AC: 128716AN: 1461034Hom.: 6604 Cov.: 36 AF XY: 0.0918 AC XY: 66700AN XY: 726828
GnomAD4 genome ? AF: 0.0764 AC: 11603AN: 151918Hom.: 529 Cov.: 30 AF XY: 0.0794 AC XY: 5893AN XY: 74252
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at