Genetic Variant CD276:n.365C>T (chr15-73713259-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000559465.1(CD276):n.365C>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 0.437 in 407,098 control chromosomes in the GnomAD database, including 39,069 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 0.43 ( 14019 hom., cov: 32)

Exomes 𝑓: 0.44 ( 25050 hom. )

Consequence

CD276
ENST00000559465.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0360

Publications

16 publications found

Variant links:

Genes affected

CD276 (HGNC:19137): (CD276 molecule) The protein encoded by this gene belongs to the immunoglobulin superfamily, and thought to participate in the regulation of T-cell-mediated immune response. Studies show that while the transcript of this gene is ubiquitously expressed in normal tissues and solid tumors, the protein is preferentially expressed only in tumor tissues. Additionally, it was observed that the 3' UTR of this transcript contains a target site for miR29 microRNA, and there is an inverse correlation between the expression of this protein and miR29 levels, suggesting regulation of expression of this gene product by miR29. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

CD276 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 (AMR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD276	NM_001024736.2 link	c.*303C>T		3_prime_UTR_variant	Exon 10 of 10	ENST00000318443.10	NP_001019907.1	Q5ZPR3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD276	ENST00000318443.10 link	c.*303C>T		3_prime_UTR_variant	Exon 10 of 10	2	NM_001024736.2	ENSP00000320084.5		Q5ZPR3-1

Frequencies

GnomAD3 genomes

AF:

0.427

AC:

64822

AN:

151886

Hom.:

14007

Cov.:

show subpopulations

Gnomad AFR

AF:

0.407

Gnomad AMI

AF:

0.387

Gnomad AMR

AF:

0.458

Gnomad ASJ

AF:

0.386

Gnomad EAS

AF:

0.357

Gnomad SAS

AF:

0.342

Gnomad FIN

AF:

0.375

Gnomad MID

AF:

0.404

Gnomad NFE

AF:

0.454

Gnomad OTH

AF:

0.428

GnomAD4 exome

AF:

0.443

AC:

112978

AN:

255094

Hom.:

25050

Cov.:

AF XY:

0.438

AC XY:

57670

AN XY:

131550

show subpopulations

African (AFR)

AF:

0.411

AC:

2728

AN:

6632

American (AMR)

AF:

0.469

AC:

3630

AN:

7740

Ashkenazi Jewish (ASJ)

AF:

0.389

AC:

3350

AN:

8614

East Asian (EAS)

AF:

0.442

AC:

6983

AN:

15812

South Asian (SAS)

AF:

0.366

AC:

7437

AN:

20326

European-Finnish (FIN)

AF:

0.397

AC:

7216

AN:

18160

Middle Eastern (MID)

AF:

0.415

AC:

517

AN:

1246

European-Non Finnish (NFE)

AF:

0.461

AC:

74089

AN:

160580

Other (OTH)

AF:

0.440

AC:

7028

AN:

15984

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

3051

6102

9154

12205

15256

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.427

AC:

64883

AN:

152004

Hom.:

14019

Cov.:

AF XY:

0.423

AC XY:

31415

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.407

AC:

16885

AN:

41452

American (AMR)

AF:

0.458

AC:

6998

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.386

AC:

1341

AN:

3472

East Asian (EAS)

AF:

0.358

AC:

1842

AN:

5152

South Asian (SAS)

AF:

0.342

AC:

1641

AN:

4802

European-Finnish (FIN)

AF:

0.375

AC:

3961

AN:

10576

Middle Eastern (MID)

AF:

0.418

AC:

122

AN:

292

European-Non Finnish (NFE)

AF:

0.454

AC:

30841

AN:

67968

Other (OTH)

AF:

0.427

AC:

901

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1928

3856

5784

7712

9640

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.436

Hom.:

25306

Bravo

AF:

0.433

Asia WGS

AF:

0.343

AC:

1193

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

9.4

(source)

DANN

Benign

0.49

PhyloP100

-0.036

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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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15-73713259-C-T

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