rs773841687

Variant names:

• chr3-47562688-A-G
• rs773841687
• NM_006574.4:c.1532T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-47562688-A-G
• chr3-47562688-A-T

Variant summary

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

The NM_006574.4(CSPG5):​c.1532T>C​(p.Ile511Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I511N) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: CSPG5 NM_006574.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.80

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.1532T>C	p.Ile511Thr	missense_variant	Exon 5 of 5	ENST00000264723.9	NP_006565.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSPG5	ENST00000264723.9	c.1532T>C	p.Ile511Thr	missense_variant	Exon 5 of 5	1	NM_006574.4	ENSP00000264723.4
CSPG5	ENST00000383738.6	c.1613T>C	p.Ile538Thr	missense_variant	Exon 5 of 5	1		ENSP00000373244.2
CSPG5	ENST00000456150.5	c.1118T>C	p.Ile373Thr	missense_variant	Exon 4 of 4	1		ENSP00000392096.1
CSPG5	ENST00000610462	c.*22T>C		3_prime_UTR_variant	Exon 4 of 4	5		ENSP00000478923.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 37

GnomAD4 genome Cov.: 31

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.82
BayesDel_addAF	Pathogenic	0.25	D
BayesDel_noAF	Uncertain	0.12
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.31	.;T;.
Eigen	Uncertain	0.25
Eigen_PC	Uncertain	0.31
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.86	D;T;T
M_CAP	Benign	0.020	T
MetaRNN	Uncertain	0.64	D;D;D
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.90	.;L;.
PrimateAI	Uncertain	0.75	T
PROVEAN	Benign	-0.67	N;N;N
REVEL	Uncertain	0.36
Sift	Uncertain	0.0020	D;D;D
Sift4G	Uncertain	0.0050	D;D;D
Polyphen		0.92, 0.87	.;P;P
Vest4		0.77
MutPred		0.55		.;Loss of stability (P = 0.0119);.;
MVP		0.59
MPC		1.4
ClinPred		0.93	D
GERP RS		3.7
Varity_R		0.21
gMVP		0.42

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

LitVar

Other links and lift over

dbSNP: rs773841687; hg19: chr3-47604178;