dbSNP rs7116432: CD44:c.*133A>G (chr11-35222511-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000610.4(CD44):c.2024+779A>G variant causes a intron 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_000610.4 intron

Scores

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: -0.322

Publications

24 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CD44	NM_000610.4 link	c.2024+779A>G		intron_variant	Intron 17 of 17	ENST00000428726.8	NP_000601.3	P16070-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD44	ENST00000428726.8 link	c.2024+779A>G		intron_variant	Intron 17 of 17	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

African (AFR)

AF:

0.222

AC:

3969

AN:

17864

American (AMR)

AF:

0.507

AC:

3504

AN:

6914

Ashkenazi Jewish (ASJ)

AF:

0.409

AC:

3813

AN:

9314

East Asian (EAS)

AF:

0.820

AC:

5675

AN:

6920

South Asian (SAS)

AF:

0.533

AC:

21529

AN:

40420

European-Finnish (FIN)

AF:

0.344

AC:

5254

AN:

15260

Middle Eastern (MID)

AF:

0.309

AC:

1144

AN:

3704

European-Non Finnish (NFE)

AF:

0.338

AC:

275329

AN:

813744

Other (OTH)

AF:

0.378

AC:

12294

AN:

32486

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.439

Heterozygous variant carriers

8426

16852

25277

33703

42129

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.349

AC:

52685

AN:

151162

Hom.:

10262

Cov.:

AF XY:

0.359

AC XY:

26519

AN XY:

73834

show subpopulations

African (AFR)

AF:

0.235

AC:

9686

AN:

41248

American (AMR)

AF:

0.432

AC:

6564

AN:

15192

Ashkenazi Jewish (ASJ)

AF:

0.416

AC:

1442

AN:

3466

East Asian (EAS)

AF:

0.815

AC:

4185

AN:

5132

South Asian (SAS)

AF:

0.558

AC:

2671

AN:

4786

European-Finnish (FIN)

AF:

0.332

AC:

3398

AN:

10250

Middle Eastern (MID)

AF:

0.306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.347

AC:

23525

AN:

67802

Other (OTH)

AF:

0.348

AC:

725

AN:

2086

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1599

3198

4797

6396

7995

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.342

Hom.:

11829

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

Calcium oxalate urolithiasis

Other:1

Mar 01, 2014

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

Significance:association

Review Status:no assertion criteria provided

Collection Method:case-control

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.1

(source)

DANN

Benign

0.76

PhyloP100

-0.32

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

rs7116432

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over