chr11-118894183-T-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001716.5(CXCR5):c.639T>A(p.His213Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,613,942 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001716.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CXCR5 | NM_001716.5 | c.639T>A | p.His213Gln | missense_variant | 2/2 | ENST00000292174.5 | |
CXCR5 | NM_032966.2 | c.504T>A | p.His168Gln | missense_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCR5 | ENST00000292174.5 | c.639T>A | p.His213Gln | missense_variant | 2/2 | 1 | NM_001716.5 | P1 | |
BCL9L | ENST00000334801.7 | c.*4232A>T | 3_prime_UTR_variant | 8/8 | 1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250956Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135670
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461842Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727216
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74292
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at