rs3732530

Variant names:

• chr3-47577463-C-A
• rs3732530
• NM_006574.4:c.563G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-47577463-C-A
• chr3-47577463-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: 𝑓 0.58 (26441 hom., cov: 31)
  • Exomes 𝑓: 0.64 (306799 hom.)
• Consequence: CSPG5 NM_006574.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 38 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006574.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSPG5	NM_006574.4	MANE Select	c.563G>T	p.Gly188Val	missense	Exon 2 of 5	NP_006565.2	O95196-2
	CSPG5	NM_001206943.2		c.563G>T	p.Gly188Val	missense	Exon 2 of 5	NP_001193872.1	O95196-1
	CSPG5	NM_001206944.2		c.563G>T	p.Gly188Val	missense	Exon 2 of 4	NP_001193873.1	A0A087WUT8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSPG5	ENST00000264723.9	TSL:1 MANE Select	c.563G>T	p.Gly188Val	missense	Exon 2 of 5	ENSP00000264723.4	O95196-2
	CSPG5	ENST00000383738.6	TSL:1	c.563G>T	p.Gly188Val	missense	Exon 2 of 5	ENSP00000373244.2	O95196-1
	CSPG5	ENST00000456150.5	TSL:1	c.149G>T	p.Gly50Val	missense	Exon 1 of 4	ENSP00000392096.1	O95196-3

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87329 AN: 151714 Hom.: 26440 Cov.: 31

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

GnomAD2 exomes AF: 0.591 AC: 148164 AN: 250842 AF XY: 0.600

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 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.: 68 AF XY: 0.641 AC XY: 465795 AN XY: 727174

African (AFR) AF: 0.397 AC: 13276 AN: 33480

American (AMR) AF: 0.391 AC: 17489 AN: 44712

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 15254 AN: 26134

East Asian (EAS) AF: 0.608 AC: 24125 AN: 39700

South Asian (SAS) AF: 0.537 AC: 46283 AN: 86258

European-Finnish (FIN) AF: 0.743 AC: 39601 AN: 53324

Middle Eastern (MID) AF: 0.582 AC: 3358 AN: 5768

European-Non Finnish (NFE) AF: 0.668 AC: 742899 AN: 1111950

Other (OTH) AF: 0.623 AC: 37627 AN: 60394

GnomAD4 genome AF: 0.575 AC: 87356 AN: 151834 Hom.: 26441 Cov.: 31 AF XY: 0.577 AC XY: 42797 AN XY: 74186

African (AFR) AF: 0.398 AC: 16486 AN: 41428

American (AMR) AF: 0.493 AC: 7526 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1980 AN: 3468

East Asian (EAS) AF: 0.601 AC: 3075 AN: 5116

South Asian (SAS) AF: 0.532 AC: 2556 AN: 4804

European-Finnish (FIN) AF: 0.749 AC: 7902 AN: 10556

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45799 AN: 67894

Other (OTH) AF: 0.570 AC: 1200 AN: 2104

Alfa AF: 0.620 Hom.: 102858

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 v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.089
BayesDel_addAF	Benign	-0.65	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	15
DANN	Benign	0.86
DEOGEN2	Benign	0.093	T
Eigen	Benign	-0.71
Eigen_PC	Benign	-0.63
FATHMM_MKL	Benign	0.13	N
LIST_S2	Benign	0.69	T
MetaRNN	Benign	0.0000018	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	0.81	L
PhyloP100		0.23
PrimateAI	Uncertain	0.53	T
PROVEAN	Benign	0.77	N
REVEL	Benign	0.018
Sift	Benign	0.24	T
Sift4G	Benign	0.23	T
Polyphen		0.028	B
Vest4		0.14
MPC		0.75
ClinPred		0.0056	T
GERP RS		0.84
Varity_R		0.090
gMVP		0.17
Mutation Taster		=98/2	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3732530; hg19: chr3-47618953; COSMIC: COSV53131417; COSMIC: COSV53131417;