rs7828552

chr8-70787972-C-T

Variant summary

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

The XM_011517527.4(XKR9):c.493+80819C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 151,898 control chromosomes in the GnomAD database, including 35,237 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 0.68 (35237 hom., cov: 32)
• Consequence: XKR9 XM_011517527.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

Genes affected

XKR9 (HGNC:20937): (XK related 9) Predicted to enable phospholipid scramblase activity. Predicted to be involved in apoptotic process involved in development; engulfment of apoptotic cell; and 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XKR9	XM_011517527.4	c.493+80819C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XKR9	ENST00000520273.1	n.353-1367C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102622 AN: 151780 Hom.: 35188 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.676 AC: 102727 AN: 151898 Hom.: 35237 Cov.: 32 AF XY: 0.669 AC XY: 49626 AN XY: 74228

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.618

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.663

Alfa AF: 0.689 Hom.: 4478

Bravo AF: 0.689

Asia WGS AF: 0.447 AC: 1558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	4.1
Dann	Benign	0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7828552; hg19: chr8-71700207;