rs12034

chr21-17569905-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001338.5(CXADR):c.*4213G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 984,758 control chromosomes in the GnomAD database, including 180,295 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 0.48 (20833 hom., cov: 32)
  • Exomes 𝑓: 0.61 (159462 hom.)
• Consequence: CXADR NM_001338.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CXADR	NM_001338.5	c.*4213G>A		3_prime_UTR_variant	7/7	ENST00000284878.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CXADR	ENST00000284878.12	c.*4213G>A		3_prime_UTR_variant	7/7	1	NM_001338.5	P2
CXADR	ENST00000400169.1	c.1017+4294G>A		intron_variant		5		A1

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72459 AN: 151866 Hom.: 20828 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.520

GnomAD4 exome AF: 0.614 AC: 510981 AN: 832776 Hom.: 159462 Cov.: 32 AF XY: 0.614 AC XY: 236091 AN XY: 384580

Gnomad4 AFR exome AF: 0.0817

Gnomad4 AMR exome AF: 0.657

Gnomad4 ASJ exome AF: 0.565

Gnomad4 EAS exome AF: 0.504

Gnomad4 SAS exome AF: 0.550

Gnomad4 FIN exome AF: 0.583

Gnomad4 NFE exome AF: 0.628

Gnomad4 OTH exome AF: 0.578

GnomAD4 genome AF: 0.477 AC: 72473 AN: 151982 Hom.: 20833 Cov.: 32 AF XY: 0.477 AC XY: 35401 AN XY: 74276

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.524

Alfa AF: 0.557 Hom.: 4111

Bravo AF: 0.462

Asia WGS AF: 0.534 AC: 1856 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	7.3
Dann	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12034; hg19: chr21-18942223;