ENST00000520273.1:n.353-975C>T

Variant names:

• chr8-70788364-C-T
• rs10504482
• ENST00000520273.1:n.353-975C>T

Variant summary

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

The ENST00000520273.1(XKR9):​n.353-975C>T 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 152,078 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: 33)
• Consequence: XKR9 ENST00000520273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 2 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=-1.01).
• 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 rank	MANE	Protein	UniProt
XKR9	XM_011517527.4	c.493+81211C>T		intron_variant	Intron 4 of 4		XP_011515829.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XKR9	ENST00000520273.1	n.353-975C>T		intron_variant	Intron 2 of 3	3
ENSG00000285579	ENST00000647843.1	n.327+81211C>T		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.0726 AC: 11031 AN: 151960 Hom.: 472 Cov.: 33

Gnomad AFR AF: 0.0604

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0551

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.0602

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0888

Gnomad OTH AF: 0.0848

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

GnomAD4 genome AF: 0.0726 AC: 11037 AN: 152078 Hom.: 474 Cov.: 33 AF XY: 0.0700 AC XY: 5203 AN XY: 74346

African (AFR) AF: 0.0603 AC: 2504 AN: 41516

American (AMR) AF: 0.0550 AC: 837 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 522 AN: 3468

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5184

South Asian (SAS) AF: 0.0398 AC: 192 AN: 4824

European-Finnish (FIN) AF: 0.0602 AC: 637 AN: 10590

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

European-Non Finnish (NFE) AF: 0.0888 AC: 6034 AN: 67954

Other (OTH) AF: 0.0834 AC: 176 AN: 2110

Alfa AF: 0.0778 Hom.: 70

Bravo AF: 0.0721

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.67
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10504482; hg19: chr8-71700599;