rs311194

chrX-2802661-A-GchrX-2802661-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001141919.2(XG):c.374-4040A>G 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 (11463 hom., 14969 hem., cov: 20)
• Consequence: XG NM_001141919.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.294

Genes affected

XG (HGNC:12806): (Xg glycoprotein (Xg blood group)) This gene encodes the XG blood group antigen, and is located at the pseudoautosomal boundary on the short (p) arm of chromosome X. The three 5' exons reside in the pseudoautosomal region and the remaining exons within the X-specific end. A truncated copy of this gene is found on the Y chromosome at the pseudoautosomal boundary. It is transcribed, but not expected to make a Y-chromosome specific gene product. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XG	NM_001141919.2	c.374-4040A>G		intron_variant		ENST00000644266.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XG	ENST00000644266.2	c.374-4040A>G		intron_variant			NM_001141919.2

Frequencies

GnomAD3 genomes AF: 0.516 AC: 54946 AN: 106542 Hom.: 11469 Cov.: 20 AF XY: 0.511 AC XY: 14952 AN XY: 29234

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.581

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.515 AC: 54946 AN: 106597 Hom.: 11463 Cov.: 20 AF XY: 0.511 AC XY: 14969 AN XY: 29297

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.552

Alfa AF: 0.563 Hom.: 5210

Bravo AF: 0.513

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.2
Dann	Benign	0.65

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: rs311194; hg19: chrX-2720702;