rs211953

Variant names:

• chr21-17517899-G-A
• rs211953
• NM_001338.5:c.43+4727G>A

Your query was ambiguous. Multiple possible variants found:

• chr21-17517899-G-A
• chr21-17517899-G-C

Variant summary

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

The NM_001338.5(CXADR):​c.43+4727G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,134 control chromosomes in the GnomAD database, including 1,850 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 0.14 (1850 hom., cov: 32)
• Consequence: CXADR NM_001338.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270

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]

BTF3L4P1 (HGNC:39645): (basic transcription factor 3 like 4 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CXADR	NM_001338.5	c.43+4727G>A		intron_variant	Intron 1 of 6	ENST00000284878.12	NP_001329.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CXADR	ENST00000284878.12	c.43+4727G>A		intron_variant	Intron 1 of 6	1	NM_001338.5	ENSP00000284878.7

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21875 AN: 152016 Hom.: 1845 Cov.: 32

Gnomad AFR AF: 0.0823

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.0323

Gnomad SAS AF: 0.0715

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.144 AC: 21900 AN: 152134 Hom.: 1850 Cov.: 32 AF XY: 0.139 AC XY: 10340 AN XY: 74350

Gnomad4 AFR AF: 0.0826

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.0323

Gnomad4 SAS AF: 0.0726

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.134

Alfa AF: 0.181 Hom.: 5410

Bravo AF: 0.139

Asia WGS AF: 0.0560 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	14
DANN	Benign	0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs211953; hg19: chr21-18890217;