X-152728131-G-A

Variant names:

• chrX-152728131-G-A
• NM_001102576.3:c.110C>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001102576.3(CSAG1):​c.110C>T​(p.Ser37Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: CSAG1 NM_001102576.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.0200
• Publications: 0 publications found

Genes affected

CSAG1 (HGNC:24294): (chondrosarcoma associated gene 1) This gene encodes a member of a family of tumor antigens. The protein is expressed in chondrosarcomas, but may also be expressed in normal tissues such as testis. Alternative splicing of this gene results in two transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.17359123).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001102576.3. 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
	CSAG1	NM_001102576.3	MANE Select	c.110C>T	p.Ser37Phe	missense	Exon 3 of 4	NP_001096046.2	Q6PB30-1
	CSAG1	NM_153478.3		c.110C>T	p.Ser37Phe	missense	Exon 4 of 5	NP_705611.2	Q6PB30-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSAG1	ENST00000452779.3	TSL:1 MANE Select	c.110C>T	p.Ser37Phe	missense	Exon 3 of 4	ENSP00000396520.2	Q6PB30-1
	CSAG1	ENST00000370287.7	TSL:1	c.110C>T	p.Ser37Phe	missense	Exon 4 of 5	ENSP00000359310.3	Q6PB30-1
	CSAG1	ENST00000370291.6	TSL:1	c.110C>T	p.Ser37Phe	missense	Exon 4 of 4	ENSP00000359314.2	Q6PB30-2

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 23

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.40
BayesDel_noAF	Benign	-0.82
CADD	Benign	14
DANN	Benign	0.93
DEOGEN2	Benign	0.036	T
LIST_S2	Benign	0.58	T
MetaRNN	Benign	0.17	T
PhyloP100		-0.020
PROVEAN	Pathogenic	-5.0	D
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.0090	D
Vest4		0.15
gMVP		0.021

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

Other links and lift over

hg19: chrX-151908871; COSMIC: COSV63400505;