chr11-35200315-T-A

Position:

• chr11-35200315-T-A

Variant summary

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

The NM_000610.4(CD44):​c.923-767T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,016 control chromosomes in the GnomAD database, including 10,788 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.35 (10788 hom., cov: 31)
• Consequence: CD44 NM_000610.4 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.900

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD44	NM_000610.4	c.923-767T>A		intron_variant		ENST00000428726.8	NP_000601.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD44	ENST00000428726.8	c.923-767T>A		intron_variant		1	NM_000610.4	ENSP00000398632	A2

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52919 AN: 151898 Hom.: 10802 Cov.: 31

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.348 AC: 52903 AN: 152016 Hom.: 10788 Cov.: 31 AF XY: 0.356 AC XY: 26451 AN XY: 74294

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.356

Alfa AF: 0.384 Hom.: 1689

Bravo AF: 0.327

Asia WGS AF: 0.510 AC: 1773 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	-0.83
CADD	Benign	3.2
DANN	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7110737; hg19: chr11-35221862;