21-17554335-C-T

Position:

• chr21-17554335-C-T

Variant summary

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

The NM_001338.5(CXADR):​c.415+2382C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 152,048 control chromosomes in the GnomAD database, including 20,746 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 (20746 hom., cov: 32)
• Consequence: CXADR NM_001338.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CXADR	NM_001338.5	c.415+2382C>T		intron_variant		ENST00000284878.12	NP_001329.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CXADR	ENST00000284878.12	c.415+2382C>T		intron_variant		1	NM_001338.5	ENSP00000284878	P2

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72347 AN: 151928 Hom.: 20741 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.476 AC: 72361 AN: 152048 Hom.: 20746 Cov.: 32 AF XY: 0.476 AC XY: 35358 AN XY: 74324

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.523

Alfa AF: 0.610 Hom.: 57502

Bravo AF: 0.461

Asia WGS AF: 0.530 AC: 1842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.45
DANN	Benign	0.61

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: rs764657; hg19: chr21-18926653;