rs7017914

Variant names:

• chr8-70678968-A-G
• rs7017914
• NM_001011720.2:c.-278-1813A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 30 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=-0.91).
• 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 rank	MANE	Protein	UniProt
XKR9	NM_001011720.2	c.-278-1813A>G		intron_variant	Intron 2 of 4	ENST00000408926.8	NP_001011720.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XKR9	ENST00000408926.8	c.-278-1813A>G		intron_variant	Intron 2 of 4	1	NM_001011720.2	ENSP00000386141.3

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

African (AFR) AF: 0.257 AC: 10660 AN: 41500

American (AMR) AF: 0.342 AC: 5230 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1650 AN: 3464

East Asian (EAS) AF: 0.0618 AC: 320 AN: 5178

South Asian (SAS) AF: 0.204 AC: 981 AN: 4820

European-Finnish (FIN) AF: 0.526 AC: 5558 AN: 10560

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35337 AN: 67940

Other (OTH) AF: 0.420 AC: 886 AN: 2110

Alfa AF: 0.476 Hom.: 48942

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
PhyloP100		-0.091
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7017914; hg19: chr8-71591203;