11-118893704-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001716.5(CXCR5):c.160G>T(p.Val54Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000347 in 1,614,128 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V54M) has been classified as Likely benign.
Frequency
Consequence
NM_001716.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.160G>T | p.Val54Leu | missense_variant | 2/2 | ENST00000292174.5 | |
CXCR5 | NM_032966.2 | c.25G>T | p.Val9Leu | missense_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXCR5 | ENST00000292174.5 | c.160G>T | p.Val54Leu | missense_variant | 2/2 | 1 | NM_001716.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000164 AC: 25AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000306 AC: 77AN: 251420Hom.: 1 AF XY: 0.000361 AC XY: 49AN XY: 135882
GnomAD4 exome AF: 0.000366 AC: 535AN: 1461860Hom.: 0 Cov.: 31 AF XY: 0.000375 AC XY: 273AN XY: 727222
GnomAD4 genome ? AF: 0.000164 AC: 25AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2022 | The c.160G>T (p.V54L) alteration is located in exon 2 (coding exon 2) of the CXCR5 gene. This alteration results from a G to T substitution at nucleotide position 160, causing the valine (V) at amino acid position 54 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at