rs2031577131

Variant names:

• chr3-47572863-T-C
• NM_006574.4:c.1205A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-47572863-T-C
• chr3-47572863-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_006574.4(CSPG5):​c.1205A>G​(p.Gln402Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000481 in 1,456,064 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000048 (0 hom.)
• Consequence: CSPG5 NM_006574.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.24

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

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSPG5	NM_006574.4	c.1205A>G	p.Gln402Arg	missense_variant	Exon 3 of 5	ENST00000264723.9	NP_006565.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSPG5	ENST00000264723.9	c.1205A>G	p.Gln402Arg	missense_variant	Exon 3 of 5	1	NM_006574.4	ENSP00000264723.4
CSPG5	ENST00000383738.6	c.1205A>G	p.Gln402Arg	missense_variant	Exon 3 of 5	1		ENSP00000373244.2
CSPG5	ENST00000456150.5	c.791A>G	p.Gln264Arg	missense_variant	Exon 2 of 4	1		ENSP00000392096.1
CSPG5	ENST00000610462.1	c.1205A>G	p.Gln402Arg	missense_variant	Exon 3 of 4	5		ENSP00000478923.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000481 AC: 7 AN: 1456064 Hom.: 0 Cov.: 31 AF XY: 0.00000829 AC XY: 6 AN XY: 723568

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000350

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000361

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.73
BayesDel_addAF	Uncertain	0.14	D
BayesDel_noAF	Uncertain	-0.030
CADD	Pathogenic	28
DANN	Uncertain	1.0
DEOGEN2	Benign	0.33	.;T;.;T
Eigen	Uncertain	0.50
Eigen_PC	Uncertain	0.46
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.96	D;D;D;D
M_CAP	Benign	0.028	D
MetaRNN	Uncertain	0.70	D;D;D;D
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.4	.;M;M;.
PrimateAI	Uncertain	0.78	T
PROVEAN	Benign	-1.1	N;N;N;.
REVEL	Benign	0.29
Sift	Uncertain	0.019	D;D;D;.
Sift4G	Pathogenic	0.0	D;D;D;D
Polyphen		0.99, 1.0	.;D;D;.
Vest4		0.85
MutPred		0.39		.;Gain of MoRF binding (P = 0.0777);Gain of MoRF binding (P = 0.0777);Gain of MoRF binding (P = 0.0777);
MVP		0.45
MPC		1.6
ClinPred		0.98	D
GERP RS		3.5
Varity_R		0.23
gMVP		0.97

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-47614353; COSMIC: COSV53130121; COSMIC: COSV53130121;