chrX-2796715-T-C

Variant names:

• chrX-2796715-T-C
• rs311183
• NM_001141919.2:c.323-595T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001141919.2(XG):​c.323-595T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0877 in 110,983 control chromosomes in the GnomAD database, including 947 homozygotes. There are 2,579 hemizygotes in GnomAD. 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 0.088 (947 hom., 2579 hem., cov: 22)
• Consequence: XG NM_001141919.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XG	NM_001141919.2	c.323-595T>C		intron_variant	Intron 6 of 10	ENST00000644266.2	NP_001135391.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XG	ENST00000644266.2	c.323-595T>C		intron_variant	Intron 6 of 10		NM_001141919.2	ENSP00000494087.1

Frequencies

GnomAD3 genomes AF: 0.0875 AC: 9702 AN: 110930 Hom.: 939 Cov.: 22

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0417

Gnomad ASJ AF: 0.0238

Gnomad EAS AF: 0.0132

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.0277

Gnomad MID AF: 0.0556

Gnomad NFE AF: 0.00397

Gnomad OTH AF: 0.0684

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

GnomAD4 genome AF: 0.0877 AC: 9738 AN: 110983 Hom.: 947 Cov.: 22 AF XY: 0.0776 AC XY: 2579 AN XY: 33237

African (AFR) AF: 0.285 AC: 8660 AN: 30370

American (AMR) AF: 0.0415 AC: 428 AN: 10321

Ashkenazi Jewish (ASJ) AF: 0.0238 AC: 63 AN: 2644

East Asian (EAS) AF: 0.0132 AC: 47 AN: 3559

South Asian (SAS) AF: 0.0125 AC: 33 AN: 2638

European-Finnish (FIN) AF: 0.0277 AC: 165 AN: 5957

Middle Eastern (MID) AF: 0.0610 AC: 13 AN: 213

European-Non Finnish (NFE) AF: 0.00397 AC: 211 AN: 53086

Other (OTH) AF: 0.0781 AC: 118 AN: 1510

Alfa AF: 0.0294 Hom.: 1651

Bravo AF: 0.0987

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.78
DANN	Benign	0.48
PhyloP100		-0.70
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs311183; hg19: chrX-2714756;