ENST00000520273.1:n.353-38464T>G

Variant names:

• chr8-70750875-T-G
• rs4581087
• ENST00000520273.1:n.353-38464T>G

Variant summary

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

The ENST00000520273.1(XKR9):​n.353-38464T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,244 control chromosomes in the GnomAD database, including 1,686 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 0.13 (1686 hom., cov: 32)
• Consequence: XKR9 ENST00000520273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 7 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XKR9	ENST00000520273.1	TSL:3	n.353-38464T>G		intron	N/A
	ENSG00000285579	ENST00000647843.1		n.327+43722T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19724 AN: 152126 Hom.: 1670 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0123

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0438

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0913

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.130 AC: 19773 AN: 152244 Hom.: 1686 Cov.: 32 AF XY: 0.126 AC XY: 9357 AN XY: 74448

African (AFR) AF: 0.240 AC: 9958 AN: 41492

American (AMR) AF: 0.115 AC: 1757 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 490 AN: 3472

East Asian (EAS) AF: 0.0125 AC: 65 AN: 5192

South Asian (SAS) AF: 0.107 AC: 518 AN: 4824

European-Finnish (FIN) AF: 0.0438 AC: 465 AN: 10626

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0913 AC: 6212 AN: 68022

Other (OTH) AF: 0.110 AC: 233 AN: 2114

Alfa AF: 0.101 Hom.: 2591

Bravo AF: 0.137

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.71
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs4581087; hg19: chr8-71663110;