8-70993352-T-G

Position:

• chr8-70993352-T-G

Variant summary

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

The XM_011517527.4(XKR9):​c.494-72005T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,940 control chromosomes in the GnomAD database, including 14,224 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 0.41 (14224 hom., cov: 31)
• Consequence: XKR9 XM_011517527.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
XKR9	XM_011517527.4	c.494-72005T>G		intron_variant			XP_011515829.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285579	ENST00000647843.1	n.328-60125T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62051 AN: 151824 Hom.: 14210 Cov.: 31

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.408 AC: 62066 AN: 151940 Hom.: 14224 Cov.: 31 AF XY: 0.410 AC XY: 30412 AN XY: 74254

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.420

Alfa AF: 0.463 Hom.: 11011

Bravo AF: 0.407

Asia WGS AF: 0.336 AC: 1172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.95
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1493202; hg19: chr8-71905587;