rs2939678

Positions:

• chr8-55334578-A-G
• chr8-55334578-A-T

Variant summary

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

The NM_052898.2(XKR4):​c.807-23100A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 152,022 control chromosomes in the GnomAD database, including 48,684 homozygotes. 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 0.79 (48684 hom., cov: 31)
• Consequence: XKR4 NM_052898.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.559

Genes affected

XKR4 (HGNC:29394): (XK related 4) Enables phospholipid scramblase activity. Involved in phosphatidylserine exposure on apoptotic cell surface. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XKR4	NM_052898.2	c.807-23100A>G		intron_variant		ENST00000327381.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XKR4	ENST00000327381.7	c.807-23100A>G		intron_variant		1	NM_052898.2	P1

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120393 AN: 151904 Hom.: 48640 Cov.: 31

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.793 AC: 120493 AN: 152022 Hom.: 48684 Cov.: 31 AF XY: 0.783 AC XY: 58190 AN XY: 74322

Gnomad4 AFR AF: 0.930

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.779

Alfa AF: 0.769 Hom.: 60753

Bravo AF: 0.794

Asia WGS AF: 0.612 AC: 2131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.1
DANN	Benign	0.40

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: rs2939678; hg19: chr8-56247138;