ENST00000425428.6:n.*1147C>T – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000425428.6(CD44):n.*1147C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 175,070 control chromosomes in the GnomAD database, including 9,503 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 0.30 ( 7971 hom., cov: 32)

Exomes 𝑓: 0.35 ( 1532 hom. )

Consequence

CD44
ENST00000425428.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.145

Publications

42 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:

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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=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD44	NM_000610.4 link	c.*438C>T		3_prime_UTR_variant	Exon 18 of 18	ENST00000428726.8	NP_000601.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD44	ENST00000428726.8 link	c.*438C>T		3_prime_UTR_variant	Exon 18 of 18	1	NM_000610.4	ENSP00000398632.2

Frequencies

GnomAD3 genomes

AF:

0.295

AC:

44895

AN:

151968

Hom.:

7974

Cov.:

show subpopulations

Gnomad AFR

AF:

0.111

Gnomad AMI

AF:

0.423

Gnomad AMR

AF:

0.325

Gnomad ASJ

AF:

0.471

Gnomad EAS

AF:

0.414

Gnomad SAS

AF:

0.605

Gnomad FIN

AF:

0.337

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.352

Gnomad OTH

AF:

0.323

GnomAD4 exome

AF:

0.348

AC:

7992

AN:

22984

Hom.:

1532

Cov.:

AF XY:

0.354

AC XY:

4277

AN XY:

12080

show subpopulations

African (AFR)

AF:

0.105

AC:

AN:

588

American (AMR)

AF:

0.345

AC:

973

AN:

2824

Ashkenazi Jewish (ASJ)

AF:

0.435

AC:

219

AN:

504

East Asian (EAS)

AF:

0.368

AC:

551

AN:

1496

South Asian (SAS)

AF:

0.518

AC:

1040

AN:

2006

European-Finnish (FIN)

AF:

0.309

AC:

337

AN:

1090

Middle Eastern (MID)

AF:

0.333

AC:

AN:

European-Non Finnish (NFE)

AF:

0.333

AC:

4421

AN:

13292

Other (OTH)

AF:

0.328

AC:

367

AN:

1118

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

253

506

758

1011

1264

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

188

282

376

470

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.295

AC:

44892

AN:

152086

Hom.:

7971

Cov.:

AF XY:

0.303

AC XY:

22498

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.111

AC:

4598

AN:

41504

American (AMR)

AF:

0.325

AC:

4961

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.471

AC:

1634

AN:

3470

East Asian (EAS)

AF:

0.414

AC:

2139

AN:

5166

South Asian (SAS)

AF:

0.604

AC:

2917

AN:

4826

European-Finnish (FIN)

AF:

0.337

AC:

3556

AN:

10558

Middle Eastern (MID)

AF:

0.347

AC:

102

AN:

294

European-Non Finnish (NFE)

AF:

0.352

AC:

23920

AN:

67978

Other (OTH)

AF:

0.322

AC:

680

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1516

3031

4547

6062

7578

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

470

940

1410

1880

2350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.334

Hom.:

21719

Bravo

AF:

0.283

Asia WGS

AF:

0.450

AC:

1562

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.66

(source)

DANN

Benign

0.23

PhyloP100

-0.14

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over