chr11-118893589-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001716.5(CXCR5):c.52-7C>G 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 0.00392 in 1,568,718 control chromosomes in the GnomAD database, including 195 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001716.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CXCR5 | NM_001716.5 | c.52-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000292174.5 | |||
CXCR5 | NM_032966.2 | c.-91C>G | 5_prime_UTR_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCR5 | ENST00000292174.5 | c.52-7C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001716.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0211 AC: 3211AN: 152196Hom.: 112 Cov.: 32
GnomAD3 exomes AF: 0.00584 AC: 1316AN: 225514Hom.: 41 AF XY: 0.00422 AC XY: 511AN XY: 121188
GnomAD4 exome AF: 0.00207 AC: 2927AN: 1416404Hom.: 83 Cov.: 31 AF XY: 0.00173 AC XY: 1210AN XY: 698446
GnomAD4 genome ? AF: 0.0212 AC: 3230AN: 152314Hom.: 112 Cov.: 32 AF XY: 0.0208 AC XY: 1547AN XY: 74486
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at