rs7828552

Variant names:

• chr8-70787972-C-T
• rs7828552
• ENST00000520273.1:n.353-1367C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000520273.1(XKR9):​n.353-1367C>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 ENST00000520273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 6 publications found

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]

ENSG00000285579 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520273.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XKR9	ENST00000520273.1	TSL:3	n.353-1367C>T		intron	N/A
	ENSG00000285579	ENST00000647843.1		n.327+80819C>T		intron	N/A

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

African (AFR) AF: 0.727 AC: 30157 AN: 41474

American (AMR) AF: 0.744 AC: 11322 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2211 AN: 3462

East Asian (EAS) AF: 0.342 AC: 1768 AN: 5174

South Asian (SAS) AF: 0.444 AC: 2138 AN: 4820

European-Finnish (FIN) AF: 0.618 AC: 6521 AN: 10552

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46348 AN: 67898

Other (OTH) AF: 0.663 AC: 1395 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.1
DANN	Benign	0.35
PhyloP100		0.0080

Splicing

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

Other links and lift over

dbSNP: rs7828552; hg19: chr8-71700207;