dbSNP rs11821102: CD44:c.*1664G>A (chr11-35230997-G-A) – 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.*1664G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0658 in 153,820 control chromosomes in the GnomAD database, including 487 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 0.066 ( 485 hom., cov: 32)

Exomes 𝑓: 0.033 ( 2 hom. )

Consequence

CD44
NM_000610.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.39

Publications

21 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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD44	NM_000610.4 link	c.*1664G>A		3_prime_UTR_variant	Exon 18 of 18	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.*1664G>A		3_prime_UTR_variant	Exon 18 of 18	1	NM_000610.4	ENSP00000398632.2		P16070-1
CD44	ENST00000263398.11 link	c.*1664G>A		3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000263398.6		P16070-12

Frequencies

GnomAD3 genomes

AF:

0.0661

AC:

10049

AN:

152058

Hom.:

482

Cov.:

show subpopulations

Gnomad AFR

AF:

0.139

Gnomad AMI

AF:

0.0912

Gnomad AMR

AF:

0.0308

Gnomad ASJ

AF:

0.0170

Gnomad EAS

AF:

0.0819

Gnomad SAS

AF:

0.0350

Gnomad FIN

AF:

0.0262

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0392

Gnomad OTH

AF:

0.0575

GnomAD4 exome

AF:

0.0328

AC:

AN:

1644

Hom.:

Cov.:

AF XY:

0.0301

AC XY:

AN XY:

898

show subpopulations

African (AFR)

AF:

0.150

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.0294

AC:

AN:

East Asian (EAS)

AF:

0.100

AC:

AN:

220

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.0185

AC:

AN:

486

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0227

AC:

AN:

794

Other (OTH)

AF:

0.0156

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.0662

AC:

10067

AN:

152176

Hom.:

485

Cov.:

AF XY:

0.0660

AC XY:

4915

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.140

AC:

5791

AN:

41500

American (AMR)

AF:

0.0306

AC:

468

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0170

AC:

AN:

3472

East Asian (EAS)

AF:

0.0822

AC:

426

AN:

5180

South Asian (SAS)

AF:

0.0345

AC:

166

AN:

4818

European-Finnish (FIN)

AF:

0.0262

AC:

278

AN:

10610

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0392

AC:

2666

AN:

67998

Other (OTH)

AF:

0.0569

AC:

120

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

465

930

1395

1860

2325

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

118

236

354

472

590

<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:

0.0485

Hom.:

798

Bravo

AF:

0.0685

Asia WGS

AF:

0.0730

AC:

252

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.1

(source)

DANN

Benign

0.50

PhyloP100

1.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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