rs1532899

Positions:

• chr8-55341021-T-C

Variant summary

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

The NM_052898.2(XKR4):​c.807-16657T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 151,988 control chromosomes in the GnomAD database, including 34,967 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 0.67 (34967 hom., cov: 31)
• Consequence: XKR4 NM_052898.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
XKR4	NM_052898.2	c.807-16657T>C		intron_variant		ENST00000327381.7	NP_443130.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
XKR4	ENST00000327381.7	c.807-16657T>C		intron_variant		1	NM_052898.2	ENSP00000328326	P1

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101434 AN: 151870 Hom.: 34953 Cov.: 31

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.668 AC: 101478 AN: 151988 Hom.: 34967 Cov.: 31 AF XY: 0.663 AC XY: 49250 AN XY: 74296

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.665

Alfa AF: 0.742 Hom.: 89524

Bravo AF: 0.657

Asia WGS AF: 0.608 AC: 2115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.62

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: rs1532899; hg19: chr8-56253581;