rs10504483

Positions:

• chr8-70789091-A-G

Variant summary

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

The XM_011517527.4(XKR9):​c.493+81938A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0726 in 152,080 control chromosomes in the GnomAD database, including 474 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 0.073 (474 hom., cov: 32)
• Consequence: XKR9 XM_011517527.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.406

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XKR9	XM_011517527.4	c.493+81938A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XKR9	ENST00000520273.1	n.353-248A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0726 AC: 11028 AN: 151962 Hom.: 472 Cov.: 32

Gnomad AFR AF: 0.0604

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0551

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0386

Gnomad FIN AF: 0.0602

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0888

Gnomad OTH AF: 0.0843

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

GnomAD4 genome AF: 0.0726 AC: 11034 AN: 152080 Hom.: 474 Cov.: 32 AF XY: 0.0700 AC XY: 5207 AN XY: 74362

Gnomad4 AFR AF: 0.0603

Gnomad4 AMR AF: 0.0550

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0401

Gnomad4 FIN AF: 0.0602

Gnomad4 NFE AF: 0.0888

Gnomad4 OTH AF: 0.0829

Alfa AF: 0.0787 Hom.: 69

Bravo AF: 0.0720

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	-0.89
CADD	Benign	13
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504483; hg19: chr8-71701326;