rs10504486

Variant names:

• chr8-70931346-A-G
• rs10504486
• ENST00000647843.1:n.328-122131A>G

Variant summary

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

The ENST00000647843.1(ENSG00000285579):​n.328-122131A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0596 in 152,180 control chromosomes in the GnomAD database, including 383 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 0.060 (383 hom., cov: 32)
• Consequence: ENSG00000285579 ENST00000647843.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763
• Publications: 1 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XKR9	XM_011517527.4	c.494-134011A>G		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.328-122131A>G		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9060 AN: 152062 Hom.: 381 Cov.: 32

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0516

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0352

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0844

Gnomad OTH AF: 0.0757

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

GnomAD4 genome AF: 0.0596 AC: 9064 AN: 152180 Hom.: 383 Cov.: 32 AF XY: 0.0569 AC XY: 4236 AN XY: 74414

African (AFR) AF: 0.0255 AC: 1059 AN: 41534

American (AMR) AF: 0.0515 AC: 786 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 515 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5172

South Asian (SAS) AF: 0.0367 AC: 177 AN: 4820

European-Finnish (FIN) AF: 0.0520 AC: 552 AN: 10606

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0844 AC: 5735 AN: 67990

Other (OTH) AF: 0.0745 AC: 157 AN: 2108

Alfa AF: 0.0682 Hom.: 55

Bravo AF: 0.0582

Asia WGS AF: 0.0140 AC: 49 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	0.23
DANN	Benign	0.60
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs10504486; hg19: chr8-71843581;