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. The variant received -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
• Publications: 3 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001166387.4. 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
	MAGEA12	NM_001166387.4	MANE Select	c.-181-240G>C		intron	N/A	NP_001159859.1
	MAGEA12	NM_001166386.3		c.-181-240G>C		intron	N/A	NP_001159858.1
	MAGEA12	NM_005367.7		c.-76+1049G>C		intron	N/A	NP_005358.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAGEA12	ENST00000393869.8	TSL:2 MANE Select	c.-181-240G>C		intron	N/A	ENSP00000377447.3
	MAGEA12	ENST00000357916.8	TSL:1	c.-76+1049G>C		intron	N/A	ENSP00000350592.4
	MAGEA12	ENST00000393900.4	TSL:1	c.-181-240G>C		intron	N/A	ENSP00000377478.3

Frequencies

GnomAD3 genomes AF: 0.522 AC: 58030 AN: 111261 Hom.: 11123 Cov.: 24

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

African (AFR) AF: 0.366 AC: 11218 AN: 30656

American (AMR) AF: 0.375 AC: 4000 AN: 10668

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1283 AN: 2646

East Asian (EAS) AF: 0.690 AC: 2400 AN: 3478

South Asian (SAS) AF: 0.618 AC: 1619 AN: 2620

European-Finnish (FIN) AF: 0.718 AC: 4306 AN: 5999

Middle Eastern (MID) AF: 0.451 AC: 97 AN: 215

European-Non Finnish (NFE) AF: 0.605 AC: 31994 AN: 52853

Other (OTH) AF: 0.479 AC: 727 AN: 1517

Alfa AF: 0.388 Hom.: 1800

Bravo AF: 0.489

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.45
PhyloP100		-0.027

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

dbSNP: rs2515832; hg19: chrX-151902054;