Variant rs7116432 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001202557.2(CD44):c.*133A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 1,097,788 control chromosomes in the GnomAD database, including 71,016 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 ( 10262 hom., cov: 29)

Exomes 𝑓: 0.35 ( 60754 hom. )

Consequence

CD44
NM_001202557.2 3_prime_UTR

Scores

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: -0.322

Variant links:

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]

CD44 links:

CD44 (HGNC:):

CD44 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD44	NM_000610.4 linkuse as main transcript	c.2024+779A>G		intron_variant		ENST00000428726.8	NP_000601.3	P16070-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD44	ENST00000428726.8 linkuse as main transcript	c.2024+779A>G		intron_variant		1	NM_000610.4	ENSP00000398632.2		P16070-1

Frequencies

GnomAD3 genomes

AF:

0.349

AC:

52685

AN:

151064

Hom.:

10267

Cov.:

show subpopulations

Gnomad AFR

AF:

0.235

Gnomad AMI

AF:

0.440

Gnomad AMR

AF:

0.432

Gnomad ASJ

AF:

0.416

Gnomad EAS

AF:

0.816

Gnomad SAS

AF:

0.558

Gnomad FIN

AF:

0.332

Gnomad MID

AF:

0.315

Gnomad NFE

AF:

0.347

Gnomad OTH

AF:

0.350

GnomAD4 exome

AF:

0.351

AC:

332511

AN:

946626

Hom.:

60754

Cov.:

AF XY:

0.355

AC XY:

160490

AN XY:

452076

show subpopulations

Gnomad4 AFR exome

AF:

0.222

Gnomad4 AMR exome

AF:

0.507

Gnomad4 ASJ exome

AF:

0.409

Gnomad4 EAS exome

AF:

0.820

Gnomad4 SAS exome

AF:

0.533

Gnomad4 FIN exome

AF:

0.344

Gnomad4 NFE exome

AF:

0.338

Gnomad4 OTH exome

AF:

0.378

GnomAD4 genome

AF:

0.349

AC:

52685

AN:

151162

Hom.:

10262

Cov.:

AF XY:

0.359

AC XY:

26519

AN XY:

73834

show subpopulations

Gnomad4 AFR

AF:

0.235

Gnomad4 AMR

AF:

0.432

Gnomad4 ASJ

AF:

0.416

Gnomad4 EAS

AF:

0.815

Gnomad4 SAS

AF:

0.558

Gnomad4 FIN

AF:

0.332

Gnomad4 NFE

AF:

0.347

Gnomad4 OTH

AF:

0.348

Alfa

AF:

0.342

Hom.:

8907

Bravo

AF:

0.350

Asia WGS

AF:

0.594

AC:

2059

AN:

3476

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Nephrolithiasis, calcium oxalate

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

-0.90

CADD

Benign

1.1

DANN

Benign

0.76

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over