11-35163005-A-T

Position:

• chr11-35163005-A-T

Variant summary

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

The NM_000610.4(CD44):​c.68-13570A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,006 control chromosomes in the GnomAD database, including 2,271 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.17 (2271 hom., cov: 32)
• Consequence: CD44 NM_000610.4 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.253

Genes affected

CD44 (HGNC:1681): (CD44 molecule (IN blood group)) The protein encoded by this gene is a cell-surface glycoprotein involved in cell-cell interactions, cell adhesion and migration. It is a receptor for hyaluronic acid (HA) and can also interact with other ligands, such as osteopontin, collagens, and matrix metalloproteinases (MMPs). This protein participates in a wide variety of cellular functions including lymphocyte activation, recirculation and homing, hematopoiesis, and tumor metastasis. Transcripts for this gene undergo complex alternative splicing that results in many functionally distinct isoforms, however, the full length nature of some of these variants has not been determined. Alternative splicing is the basis for the structural and functional diversity of this protein, and may be related to tumor metastasis. [provided by RefSeq, Jul 2008]

SNORD164 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD44	NM_000610.4	c.68-13570A>T		intron_variant		ENST00000428726.8
SNORD164	NR_145794.1	n.56A>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD44	ENST00000428726.8	c.68-13570A>T		intron_variant		1	NM_000610.4	A2

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25051 AN: 151888 Hom.: 2258 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0360

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.165 AC: 25091 AN: 152006 Hom.: 2271 Cov.: 32 AF XY: 0.166 AC XY: 12372 AN XY: 74312

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.0359

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.172

Alfa AF: 0.148 Hom.: 259

Bravo AF: 0.172

Asia WGS AF: 0.151 AC: 528 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Calcium oxalate urolithiasis Other:1

association, no assertion criteria provided

case-control

Division of Molecular Genetics and Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University

Mar 01, 2014

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.3
DANN	Benign	0.84

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: rs353637; hg19: chr11-35184552;