dbSNP rs3732530: CSPG5:p.Gly188Val (chr3-47577463-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006574.4(CSPG5):c.563G>T(p.Gly188Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 1,613,554 control chromosomes in the GnomAD database, including 333,240 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.58 ( 26441 hom., cov: 31)

Exomes 𝑓: 0.64 ( 306799 hom. )

Consequence

CSPG5
NM_006574.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.232

Variant links:

Genes affected

CSPG5 (HGNC:2467): (chondroitin sulfate proteoglycan 5) The protein encoded by this gene is a proteoglycan that may function as a neural growth and differentiation factor. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2011]

CSPG5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.765501E-6).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSPG5	NM_006574.4 link	c.563G>T	p.Gly188Val	missense_variant	Exon 2 of 5	ENST00000264723.9	NP_006565.2	O95196-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSPG5	ENST00000264723.9 link	c.563G>T	p.Gly188Val	missense_variant	Exon 2 of 5	1	NM_006574.4	ENSP00000264723.4		O95196-2

Frequencies

GnomAD3 genomes

AF:

0.576

AC:

87329

AN:

151714

Hom.:

26440

Cov.:

show subpopulations

Gnomad AFR

AF:

0.398

Gnomad AMI

AF:

0.711

Gnomad AMR

AF:

0.494

Gnomad ASJ

AF:

0.571

Gnomad EAS

AF:

0.602

Gnomad SAS

AF:

0.532

Gnomad FIN

AF:

0.749

Gnomad MID

AF:

0.627

Gnomad NFE

AF:

0.675

Gnomad OTH

AF:

0.577

GnomAD3 exomes

AF:

0.591

AC:

148164

AN:

250842

Hom.:

45791

AF XY:

0.600

AC XY:

81409

AN XY:

135762

show subpopulations

Gnomad AFR exome

AF:

0.400

Gnomad AMR exome

AF:

0.371

Gnomad ASJ exome

AF:

0.575

Gnomad EAS exome

AF:

0.593

Gnomad SAS exome

AF:

0.538

Gnomad FIN exome

AF:

0.746

Gnomad NFE exome

AF:

0.669

Gnomad OTH exome

AF:

0.602

GnomAD4 exome

AF:

0.643

AC:

939912

AN:

1461720

Hom.:

306799

Cov.:

AF XY:

0.641

AC XY:

465795

AN XY:

727174

show subpopulations

Gnomad4 AFR exome

AF:

0.397

Gnomad4 AMR exome

AF:

0.391

Gnomad4 ASJ exome

AF:

0.584

Gnomad4 EAS exome

AF:

0.608

Gnomad4 SAS exome

AF:

0.537

Gnomad4 FIN exome

AF:

0.743

Gnomad4 NFE exome

AF:

0.668

Gnomad4 OTH exome

AF:

0.623

GnomAD4 genome

AF:

0.575

AC:

87356

AN:

151834

Hom.:

26441

Cov.:

AF XY:

0.577

AC XY:

42797

AN XY:

74186

show subpopulations

Gnomad4 AFR

AF:

0.398

Gnomad4 AMR

AF:

0.493

Gnomad4 ASJ

AF:

0.571

Gnomad4 EAS

AF:

0.601

Gnomad4 SAS

AF:

0.532

Gnomad4 FIN

AF:

0.749

Gnomad4 NFE

AF:

0.675

Gnomad4 OTH

AF:

0.570

Alfa

AF:

0.635

Hom.:

65903

Bravo

AF:

0.546

TwinsUK

AF:

0.652

AC:

2419

ALSPAC

AF:

0.672

AC:

2589

ESP6500AA

AF:

0.388

AC:

1711

ESP6500EA

AF:

0.657

AC:

5653

ExAC

AF:

0.594

AC:

72071

Asia WGS

AF:

0.546

AC:

1902

AN:

3478

EpiCase

AF:

0.651

EpiControl

AF:

0.652

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.089

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Benign

0.86

DEOGEN2

Benign

0.093

.;T;.;T

Eigen

Benign

-0.71

Eigen_PC

Benign

-0.63

FATHMM_MKL

Benign

0.13

LIST_S2

Benign

0.69

T;T;T;T

MetaRNN

Benign

0.0000018

T;T;T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

0.81

.;L;L;.

PrimateAI

Uncertain

0.53

PROVEAN

Benign

0.77

N;N;N;.

REVEL

Benign

0.018

Sift

Benign

0.24

T;T;T;.

Sift4G

Benign

0.23

T;T;T;T

Polyphen

0.028, 0.0050

.;B;B;.

Vest4

0.14

MPC

0.75

ClinPred

0.0056

GERP RS

0.84

Varity_R

0.090

gMVP

0.17

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over