rs381861
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001207066.2(CXADR):c.1017+4525A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 985,188 control chromosomes in the GnomAD database, including 7,880 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.11 ( 971 hom., cov: 32)
Exomes 𝑓: 0.13 ( 6909 hom. )
Consequence
CXADR
NM_001207066.2 intron
NM_001207066.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.663
Genes affected
CXADR (HGNC:2559): (CXADR Ig-like cell adhesion molecule) The protein encoded by this gene is a type I membrane receptor for group B coxsackieviruses and subgroup C adenoviruses. Several transcript variants encoding different isoforms have been found for this gene. Pseudogenes of this gene are found on chromosomes 15, 18, and 21. [provided by RefSeq, May 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CXADR | NM_001338.5 | downstream_gene_variant | ENST00000284878.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXADR | ENST00000400169.1 | c.1017+4525A>T | intron_variant | 5 | A1 | ||||
CXADR | ENST00000284878.12 | downstream_gene_variant | 1 | NM_001338.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.110 AC: 16715AN: 152076Hom.: 969 Cov.: 32
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GnomAD4 exome AF: 0.128 AC: 106299AN: 832994Hom.: 6909 Cov.: 32 AF XY: 0.128 AC XY: 49300AN XY: 384662
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GnomAD4 genome ? AF: 0.110 AC: 16729AN: 152194Hom.: 971 Cov.: 32 AF XY: 0.107 AC XY: 7987AN XY: 74418
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at