ENST00000647843.1:n.328-90647C>T

Variant names:

• chr8-70962830-C-T
• rs10504490
• ENST00000647843.1:n.328-90647C>T

Variant summary

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

The ENST00000647843.1(ENSG00000285579):​n.328-90647C>T 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 152,256 control chromosomes in the GnomAD database, including 382 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 (382 hom., cov: 32)
• Consequence: ENSG00000285579 ENST00000647843.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• 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=-0.82).
• 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.494-102527C>T		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.328-90647C>T		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9068 AN: 152138 Hom.: 380 Cov.: 32

Gnomad AFR AF: 0.0256

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0516

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0358

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: 9072 AN: 152256 Hom.: 382 Cov.: 32 AF XY: 0.0570 AC XY: 4241 AN XY: 74450

African (AFR) AF: 0.0255 AC: 1060 AN: 41548

American (AMR) AF: 0.0515 AC: 787 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 515 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0373 AC: 180 AN: 4824

European-Finnish (FIN) AF: 0.0520 AC: 551 AN: 10588

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

European-Non Finnish (NFE) AF: 0.0844 AC: 5739 AN: 68028

Other (OTH) AF: 0.0744 AC: 157 AN: 2110

Alfa AF: 0.0683 Hom.: 55

Bravo AF: 0.0583

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	-0.82
CADD	Benign	4.4
DANN	Benign	0.51
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs10504490; hg19: chr8-71875065;