rs7017914

Positions:

• chr8-70678968-A-G

Variant summary

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

The NM_001011720.2(XKR9):​c.-278-1813A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 152,052 control chromosomes in the GnomAD database, including 13,896 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 0.40 (13896 hom., cov: 32)
• Consequence: XKR9 NM_001011720.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XKR9	NM_001011720.2	c.-278-1813A>G		intron_variant		ENST00000408926.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XKR9	ENST00000408926.8	c.-278-1813A>G		intron_variant		1	NM_001011720.2	P1

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61286 AN: 151934 Hom.: 13890 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.403 AC: 61301 AN: 152052 Hom.: 13896 Cov.: 32 AF XY: 0.399 AC XY: 29626 AN XY: 74310

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.0618

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.420

Alfa AF: 0.490 Hom.: 15685

Bravo AF: 0.382

Asia WGS AF: 0.149 AC: 519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.6
DANN	Benign	0.87

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7017914; hg19: chr8-71591203;