X-152734908-G-C

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001166387.4(MAGEA12):​c.-181-240G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: 𝑓 0.52 (11115 hom., 17564 hem., cov: 24)
  • Failed GnomAD Quality Control
• 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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAGEA12	NM_001166387.4	c.-181-240G>C		intron_variant	Intron 1 of 2	ENST00000393869.8	NP_001159859.1
MAGEA12	NM_001166386.3	c.-181-240G>C		intron_variant	Intron 1 of 2		NP_001159858.1
MAGEA12	NM_005367.7	c.-76+1049G>C		intron_variant	Intron 1 of 1		NP_005358.2
CSAG4	NR_073432.1	n.33+1049G>C		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>C		intron_variant	Intron 1 of 2	2	NM_001166387.4	ENSP00000377447.3
MAGEA12	ENST00000357916.8	c.-76+1049G>C		intron_variant	Intron 1 of 1	1		ENSP00000350592.4
MAGEA12	ENST00000393900.4	c.-181-240G>C		intron_variant	Intron 1 of 2	1		ENSP00000377478.3
CSAG4	ENST00000361201.8	n.33+1049G>C		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.522 AC: 58030 AN: 111261 Hom.: 11123 Cov.: 24 AF XY: 0.524 AC XY: 17551 AN XY: 33519

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.475

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.521 AC: 58022 AN: 111320 Hom.: 11115 Cov.: 24 AF XY: 0.523 AC XY: 17564 AN XY: 33588

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.479

Alfa AF: 0.388 Hom.: 1800

Bravo AF: 0.489

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.45

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;