rs2824374

Positions:

• chr21-17585313-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001207066.2(CXADR):​c.1018-7839A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0958 in 152,174 control chromosomes in the GnomAD database, including 919 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 0.096 (919 hom., cov: 32)
• Consequence: CXADR NM_001207066.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CXADR	NM_001207066.2	c.1018-7839A>G		intron_variant
CXADR	XM_011529476.3	c.1017+19702A>G		intron_variant
CXADR	XM_011529477.3	c.756-7839A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CXADR	ENST00000400169.1	c.1018-7839A>G		intron_variant		5		A1

Frequencies

GnomAD3 genomes AF: 0.0957 AC: 14554 AN: 152056 Hom.: 919 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.0902

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0345

Gnomad FIN AF: 0.0625

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0535

Gnomad OTH AF: 0.109

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0958 AC: 14573 AN: 152174 Hom.: 919 Cov.: 32 AF XY: 0.0949 AC XY: 7060 AN XY: 74414

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.0901

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.0346

Gnomad4 FIN AF: 0.0625

Gnomad4 NFE AF: 0.0535

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0689 Hom.: 362

Bravo AF: 0.103

Asia WGS AF: 0.0710 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.42
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2824374; hg19: chr21-18957631;