chrX-152740352-C-T

Variant names:

• chrX-152740352-C-T
• rs200202883
• ENST00000361201.8:n.332C>T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP6

The ENST00000361201.8(CSAG4):​n.332C>T variant causes a non coding transcript exon 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 Likely benign (no stars).

• Frequency: Genomes: not found (cov: 22)
• Consequence: CSAG4 ENST00000361201.8 non_coding_transcript_exon
• Clinical Significance: Likely benign no assertion criteria provided B:2
• Conservation: PhyloP100: 0.656
• Publications: 1 publications found

Genes affected

CSAG4 (HGNC:):

CSAG4 (HGNC:20923): (CSAG family member 4 (pseudogene))

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant X-152740352-C-T is Benign according to our data. Variant chrX-152740352-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 1206311.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000361201.8. 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
	CSAG4	NR_073432.1		n.332C>T		non_coding_transcript_exon	Exon 3 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSAG4	ENST00000361201.8	TSL:2	n.332C>T		non_coding_transcript_exon	Exon 3 of 4
	CSAG4	ENST00000583763.1	TSL:6	n.118C>T		non_coding_transcript_exon	Exon 2 of 3

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 22

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.5
DANN	Benign	0.86
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs200202883; hg19: chrX-151896609;