Genetic Variant CSPG4:c.*796T>C (chr15-75674754-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_001897.5(CSPG4):c.*796T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 398,370 control chromosomes in the GnomAD database, including 55,532 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 0.51 ( 20094 hom., cov: 32)

Exomes 𝑓: 0.53 ( 35438 hom. )

Consequence

CSPG4
NM_001897.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.290

Publications

10 publications found

Variant links:

Genes affected

CSPG4 (HGNC:2466): (chondroitin sulfate proteoglycan 4) A human melanoma-associated chondroitin sulfate proteoglycan plays a role in stabilizing cell-substratum interactions during early events of melanoma cell spreading on endothelial basement membranes. CSPG4 represents an integral membrane chondroitin sulfate proteoglycan expressed by human malignant melanoma cells. [provided by RefSeq, Jul 2008]

CSPG4 Gene-Disease associations (from GenCC):

schizophrenia
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

CSPG4 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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSPG4	NM_001897.5 link	c.*796T>C		3_prime_UTR_variant	Exon 10 of 10	ENST00000308508.5	NP_001888.2	Q6UVK1
CSPG4	XM_047432196.1 link	c.*796T>C		3_prime_UTR_variant	Exon 10 of 10		XP_047288152.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSPG4	ENST00000308508.5 link	c.*796T>C		3_prime_UTR_variant	Exon 10 of 10	1	NM_001897.5	ENSP00000312506.5		Q6UVK1

Frequencies

GnomAD3 genomes

AF:

0.509

AC:

77298

AN:

151818

Hom.:

20083

Cov.:

show subpopulations

Gnomad AFR

AF:

0.423

Gnomad AMI

AF:

0.636

Gnomad AMR

AF:

0.539

Gnomad ASJ

AF:

0.585

Gnomad EAS

AF:

0.314

Gnomad SAS

AF:

0.473

Gnomad FIN

AF:

0.512

Gnomad MID

AF:

0.614

Gnomad NFE

AF:

0.565

Gnomad OTH

AF:

0.521

GnomAD4 exome

AF:

0.529

AC:

130468

AN:

246434

Hom.:

35438

Cov.:

AF XY:

0.531

AC XY:

66284

AN XY:

124896

show subpopulations

African (AFR)

AF:

0.421

AC:

3026

AN:

7180

American (AMR)

AF:

0.545

AC:

4055

AN:

7436

Ashkenazi Jewish (ASJ)

AF:

0.585

AC:

5403

AN:

9240

East Asian (EAS)

AF:

0.290

AC:

6637

AN:

22894

South Asian (SAS)

AF:

0.485

AC:

1470

AN:

3034

European-Finnish (FIN)

AF:

0.525

AC:

10973

AN:

20902

Middle Eastern (MID)

AF:

0.538

AC:

696

AN:

1294

European-Non Finnish (NFE)

AF:

0.566

AC:

89464

AN:

158082

Other (OTH)

AF:

0.534

AC:

8744

AN:

16372

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

3332

6664

9996

13328

16660

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

342

684

1026

1368

1710

<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:

0.509

AC:

77343

AN:

151936

Hom.:

20094

Cov.:

AF XY:

0.505

AC XY:

37464

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.423

AC:

17514

AN:

41412

American (AMR)

AF:

0.539

AC:

8247

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.585

AC:

2029

AN:

3466

East Asian (EAS)

AF:

0.313

AC:

1610

AN:

5152

South Asian (SAS)

AF:

0.473

AC:

2279

AN:

4818

European-Finnish (FIN)

AF:

0.512

AC:

5406

AN:

10560

Middle Eastern (MID)

AF:

0.616

AC:

181

AN:

294

European-Non Finnish (NFE)

AF:

0.565

AC:

38407

AN:

67928

Other (OTH)

AF:

0.518

AC:

1090

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1925

3849

5774

7698

9623

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

680

1360

2040

2720

3400

<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:

0.554

Hom.:

72391

Bravo

AF:

0.506

Asia WGS

AF:

0.382

AC:

1333

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.2

(source)

DANN

Benign

0.61

PhyloP100

-0.29

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