rs311194

Variant names:

• chrX-2802661-A-G
• rs311194
• NM_001141919.2:c.374-4040A>G

Your query was ambiguous. Multiple possible variants found:

• chrX-2802661-A-G
• chrX-2802661-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
XG	NM_001141919.2	c.374-4040A>G		intron_variant	Intron 7 of 10	ENST00000644266.2	NP_001135391.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XG	ENST00000644266.2	c.374-4040A>G		intron_variant	Intron 7 of 10		NM_001141919.2	ENSP00000494087.1

Frequencies

GnomAD3 genomes AF: 0.516 AC: 54946 AN: 106542 Hom.: 11469 Cov.: 20

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

African (AFR) AF: 0.257 AC: 7485 AN: 29164

American (AMR) AF: 0.683 AC: 6715 AN: 9829

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 1604 AN: 2587

East Asian (EAS) AF: 0.418 AC: 1410 AN: 3377

South Asian (SAS) AF: 0.383 AC: 881 AN: 2300

European-Finnish (FIN) AF: 0.559 AC: 3001 AN: 5365

Middle Eastern (MID) AF: 0.579 AC: 121 AN: 209

European-Non Finnish (NFE) AF: 0.629 AC: 32525 AN: 51676

Other (OTH) AF: 0.552 AC: 792 AN: 1434

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
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

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: rs311194; hg19: chrX-2720702;