rs2515832

Variant names:

• chrX-152734908-G-A
• rs2515832
• NM_001166387.4:c.-181-240G>A

Your query was ambiguous. Multiple possible variants found:

• chrX-152734908-G-A
• chrX-152734908-G-C
• chrX-152734908-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001166387.4(MAGEA12):​c.-181-240G>A variant causes a intron 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 24)
• Consequence: MAGEA12 NM_001166387.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

Genes affected

MAGEA12 (HGNC:6799): (MAGE family member A12) This gene is closely related to several other genes clustered on chromosome X. These genes may be overexpressed in tumors. Multiple alternatively spliced variants encoding the same protein have been identified. [provided by RefSeq, Jun 2014]

CSAG4 (HGNC:):

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

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAGEA12	NM_001166387.4	c.-181-240G>A		intron_variant	Intron 1 of 2	ENST00000393869.8	NP_001159859.1
MAGEA12	NM_001166386.3	c.-181-240G>A		intron_variant	Intron 1 of 2		NP_001159858.1
MAGEA12	NM_005367.7	c.-76+1049G>A		intron_variant	Intron 1 of 1		NP_005358.2
CSAG4	NR_073432.1	n.33+1049G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAGEA12	ENST00000393869.8	c.-181-240G>A		intron_variant	Intron 1 of 2	2	NM_001166387.4	ENSP00000377447.3
MAGEA12	ENST00000357916.8	c.-76+1049G>A		intron_variant	Intron 1 of 1	1		ENSP00000350592.4
MAGEA12	ENST00000393900.4	c.-181-240G>A		intron_variant	Intron 1 of 2	1		ENSP00000377478.3
CSAG4	ENST00000361201.8	n.33+1049G>A		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes Cov.: 24

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 24

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	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: rs2515832; hg19: chrX-151902054;