dbSNP rs3181301: CD9:c.621+343C>A (chr12-6236618-C-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_001769.4(CD9):c.621+343C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 420,900 control chromosomes in the GnomAD database, including 51,294 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 0.46 ( 16683 hom., cov: 33)

Exomes 𝑓: 0.50 ( 34611 hom. )

Consequence

CD9
NM_001769.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0290

Publications

12 publications found

Variant links:

Genes affected

CD9 (HGNC:1709): (CD9 molecule) This gene encodes a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Tetraspanins are cell surface glycoproteins with four transmembrane domains that form multimeric complexes with other cell surface proteins. The encoded protein functions in many cellular processes including differentiation, adhesion, and signal transduction, and expression of this gene plays a critical role in the suppression of cancer cell motility and metastasis. [provided by RefSeq, Jan 2011]

CD9 links:

ENSG00000305396 (HGNC:):

ENSG00000305396 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=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD9	NM_001769.4 link	c.621+343C>A		intron_variant	Intron 7 of 7	ENST00000009180.10	NP_001760.1	P21926

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD9	ENST00000009180.10 link	c.621+343C>A		intron_variant	Intron 7 of 7	1	NM_001769.4	ENSP00000009180.4		P21926

Frequencies

GnomAD3 genomes

AF:

0.464

AC:

70598

AN:

151996

Hom.:

16669

Cov.:

show subpopulations

Gnomad AFR

AF:

0.374

Gnomad AMI

AF:

0.522

Gnomad AMR

AF:

0.451

Gnomad ASJ

AF:

0.596

Gnomad EAS

AF:

0.421

Gnomad SAS

AF:

0.469

Gnomad FIN

AF:

0.490

Gnomad MID

AF:

0.560

Gnomad NFE

AF:

0.512

Gnomad OTH

AF:

0.494

GnomAD4 exome

AF:

0.504

AC:

135447

AN:

268784

Hom.:

34611

Cov.:

AF XY:

0.504

AC XY:

69111

AN XY:

137056

show subpopulations

African (AFR)

AF:

0.376

AC:

3032

AN:

8054

American (AMR)

AF:

0.438

AC:

4250

AN:

9706

Ashkenazi Jewish (ASJ)

AF:

0.597

AC:

5821

AN:

9746

East Asian (EAS)

AF:

0.443

AC:

10673

AN:

24084

South Asian (SAS)

AF:

0.472

AC:

2779

AN:

5886

European-Finnish (FIN)

AF:

0.494

AC:

10529

AN:

21328

Middle Eastern (MID)

AF:

0.644

AC:

883

AN:

1372

European-Non Finnish (NFE)

AF:

0.518

AC:

88623

AN:

171224

Other (OTH)

AF:

0.509

AC:

8857

AN:

17384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

3366

6733

10099

13466

16832

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

420

840

1260

1680

2100

<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:

0.464

AC:

70642

AN:

152116

Hom.:

16683

Cov.:

AF XY:

0.463

AC XY:

34430

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.374

AC:

15532

AN:

41492

American (AMR)

AF:

0.451

AC:

6903

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.596

AC:

2067

AN:

3470

East Asian (EAS)

AF:

0.422

AC:

2176

AN:

5162

South Asian (SAS)

AF:

0.469

AC:

2259

AN:

4816

European-Finnish (FIN)

AF:

0.490

AC:

5189

AN:

10592

Middle Eastern (MID)

AF:

0.561

AC:

165

AN:

294

European-Non Finnish (NFE)

AF:

0.512

AC:

34829

AN:

67982

Other (OTH)

AF:

0.497

AC:

1047

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1975

3951

5926

7902

9877

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

660

1320

1980

2640

3300

<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:

0.483

Hom.:

9405

Bravo

AF:

0.461

Asia WGS

AF:

0.413

AC:

1437

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.78

(source)

DANN

Benign

0.55

PhyloP100

0.029

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