ENST00000647843.1:n.328-142010G>A

Variant names:

• chr8-70911467-G-A
• rs10504485
• ENST00000647843.1:n.328-142010G>A

Variant summary

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

The ENST00000647843.1(ENSG00000285579):​n.328-142010G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0838 in 152,206 control chromosomes in the GnomAD database, including 609 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 0.084 (609 hom., cov: 32)
• Consequence: ENSG00000285579 ENST00000647843.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 3 publications found

Genes affected

ENSG00000285579 (HGNC:):

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XKR9	XM_011517527.4	c.494-153890G>A		intron_variant	Intron 4 of 4		XP_011515829.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285579	ENST00000647843.1	n.328-142010G>A		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.0838 AC: 12742 AN: 152088 Hom.: 605 Cov.: 32

Gnomad AFR AF: 0.0971

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0621

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0389

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.0838 AC: 12755 AN: 152206 Hom.: 609 Cov.: 32 AF XY: 0.0807 AC XY: 6005 AN XY: 74400

African (AFR) AF: 0.0971 AC: 4031 AN: 41534

American (AMR) AF: 0.0619 AC: 945 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 526 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0404 AC: 195 AN: 4826

European-Finnish (FIN) AF: 0.0603 AC: 639 AN: 10596

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0896 AC: 6094 AN: 68014

Other (OTH) AF: 0.0899 AC: 190 AN: 2114

Alfa AF: 0.0866 Hom.: 82

Bravo AF: 0.0844

Asia WGS AF: 0.0160 AC: 57 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.14
DANN	Benign	0.37
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10504485; hg19: chr8-71823702;