chr8-55382802-G-A

Position:

• chr8-55382802-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.1006+24925G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 151,838 control chromosomes in the GnomAD database, including 1,638 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 0.10 (1638 hom., cov: 32)
• Consequence: XKR4 NM_052898.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XKR4	NM_052898.2	c.1006+24925G>A		intron_variant		ENST00000327381.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XKR4	ENST00000327381.7	c.1006+24925G>A		intron_variant		1	NM_052898.2	P1

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15268 AN: 151722 Hom.: 1639 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0614

Gnomad ASJ AF: 0.0593

Gnomad EAS AF: 0.0116

Gnomad SAS AF: 0.0446

Gnomad FIN AF: 0.0227

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.0338

Gnomad OTH AF: 0.0917

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

GnomAD4 genome AF: 0.101 AC: 15292 AN: 151838 Hom.: 1638 Cov.: 32 AF XY: 0.0975 AC XY: 7232 AN XY: 74200

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.0612

Gnomad4 ASJ AF: 0.0593

Gnomad4 EAS AF: 0.0116

Gnomad4 SAS AF: 0.0443

Gnomad4 FIN AF: 0.0227

Gnomad4 NFE AF: 0.0338

Gnomad4 OTH AF: 0.0912

Alfa AF: 0.0217 Hom.: 32

Bravo AF: 0.112

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.29

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: rs951255; hg19: chr8-56295362;