X-152728080-G-A

Variant names:

• chrX-152728080-G-A
• rs1556830729
• NM_001102576.3:c.161C>T

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Moderate BS2

The NM_001102576.3(CSAG1):​c.161C>T​(p.Pro54Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000234 in 1,208,797 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 79 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 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. P54R) has been classified as Benign.

• Frequency:
  • Genomes: 𝑓 0.0013 (0 hom., 41 hem., cov: 22)
  • Exomes 𝑓: 0.00013 (0 hom. 38 hem.)
• Consequence: CSAG1 NM_001102576.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• 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: Likely_benign. The variant received -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.18171942).
• BS2: High Hemizygotes in GnomAd4 at 41 gene

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.161C>T	p.Pro54Leu	missense	Exon 3 of 4	NP_001096046.2	Q6PB30-1
	CSAG1	NM_153478.3		c.161C>T	p.Pro54Leu	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.161C>T	p.Pro54Leu	missense	Exon 3 of 4	ENSP00000396520.2	Q6PB30-1
	CSAG1	ENST00000370287.7	TSL:1	c.161C>T	p.Pro54Leu	missense	Exon 4 of 5	ENSP00000359310.3	Q6PB30-1
	CSAG1	ENST00000370291.6	TSL:1	c.161C>T	p.Pro54Leu	missense	Exon 4 of 4	ENSP00000359314.2	Q6PB30-2

Frequencies

GnomAD3 genomes AF: 0.00127 AC: 141 AN: 110762 Hom.: 0 Cov.: 22

Gnomad AFR AF: 0.00449

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000384

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000668

GnomAD2 exomes AF: 0.000431 AC: 79 AN: 183295 AF XY: 0.000309

Gnomad AFR exome AF: 0.00585

Gnomad AMR exome AF: 0.0000365

Gnomad ASJ exome AF: 0.000134

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000128 AC: 140 AN: 1097984 Hom.: 0 Cov.: 33 AF XY: 0.000105 AC XY: 38 AN XY: 363458

African (AFR) AF: 0.00451 AC: 119 AN: 26394

American (AMR) AF: 0.000114 AC: 4 AN: 35199

Ashkenazi Jewish (ASJ) AF: 0.0000516 AC: 1 AN: 19382

East Asian (EAS) AF: 0.00 AC: 0 AN: 30205

South Asian (SAS) AF: 0.00 AC: 0 AN: 54118

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40532

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4131

European-Non Finnish (NFE) AF: 0.00000238 AC: 2 AN: 841938

Other (OTH) AF: 0.000304 AC: 14 AN: 46085

GnomAD4 genome AF: 0.00129 AC: 143 AN: 110813 Hom.: 0 Cov.: 22 AF XY: 0.00124 AC XY: 41 AN XY: 33045

African (AFR) AF: 0.00455 AC: 138 AN: 30335

American (AMR) AF: 0.000384 AC: 4 AN: 10425

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2634

East Asian (EAS) AF: 0.00 AC: 0 AN: 3518

South Asian (SAS) AF: 0.00 AC: 0 AN: 2556

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5979

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 216

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 52950

Other (OTH) AF: 0.000660 AC: 1 AN: 1515

Alfa AF: 0.0000877 Hom.: 1

Bravo AF: 0.00145

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_noAF	Benign	-0.79
CADD	Benign	15
DANN	Benign	0.87
DEOGEN2	Benign	0.037	T
LIST_S2	Benign	0.64	T
MetaRNN	Benign	0.18	T
PhyloP100		-0.017
PROVEAN	Pathogenic	-10	D
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Vest4		0.27
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
gMVP		0.012

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1556830729; hg19: chrX-151908922;