rs2824374

Variant names:

• chr21-17585313-A-G
• rs2824374
• NM_001207066.2:c.1018-7839A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CXADR	NM_001207066.2	c.1018-7839A>G		intron_variant	Intron 7 of 7		NP_001193995.1
CXADR	XM_011529476.3	c.1017+19702A>G		intron_variant	Intron 7 of 7		XP_011527778.1
CXADR	XM_011529477.3	c.756-7839A>G		intron_variant	Intron 5 of 5		XP_011527779.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CXADR	ENST00000400169.1	c.1018-7839A>G		intron_variant	Intron 7 of 7	5		ENSP00000383033.1

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

African (AFR) AF: 0.178 AC: 7387 AN: 41492

American (AMR) AF: 0.0901 AC: 1378 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0519 AC: 180 AN: 3468

East Asian (EAS) AF: 0.141 AC: 728 AN: 5168

South Asian (SAS) AF: 0.0346 AC: 167 AN: 4830

European-Finnish (FIN) AF: 0.0625 AC: 663 AN: 10606

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0535 AC: 3640 AN: 68002

Other (OTH) AF: 0.107 AC: 227 AN: 2116

Alfa AF: 0.0692 Hom.: 417

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
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2824374; hg19: chr21-18957631;