rs2622590

chr8-55445714-G-A

Variant summary

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

The NM_052898.2(XKR4):c.1007-77567G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,086 control chromosomes in the GnomAD database, including 2,256 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 0.15 (2256 hom., cov: 32)
• Consequence: XKR4 NM_052898.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XKR4	NM_052898.2	c.1007-77567G>A		intron_variant		ENST00000327381.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XKR4	ENST00000327381.7	c.1007-77567G>A		intron_variant		1	NM_052898.2	P1

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23078 AN: 151966 Hom.: 2247 Cov.: 32

Gnomad AFR AF: 0.0956

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.152 AC: 23117 AN: 152086 Hom.: 2256 Cov.: 32 AF XY: 0.158 AC XY: 11741 AN XY: 74356

Gnomad4 AFR AF: 0.0962

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.142

Alfa AF: 0.143 Hom.: 2073

Bravo AF: 0.154

Asia WGS AF: 0.336 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.0
Dann	Benign	0.52

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: rs2622590; hg19: chr8-56358274;