rs11783247

Positions:

• chr8-10931365-C-T

Variant summary

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

The NM_173683.4(XKR6):​c.765-6535G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 151,914 control chromosomes in the GnomAD database, including 23,433 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 0.53 (23433 hom., cov: 32)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440

Genes affected

XKR6 (HGNC:27806): (XK related 6) 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XKR6	NM_173683.4	c.765-6535G>A		intron_variant		ENST00000416569.3
XKR6	XM_024447129.2	c.765-6535G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XKR6	ENST00000416569.3	c.765-6535G>A		intron_variant		1	NM_173683.4	P1
XKR6	ENST00000382461.8	c.-13-6535G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81014 AN: 151798 Hom.: 23405 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.0325

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.534 AC: 81089 AN: 151914 Hom.: 23433 Cov.: 32 AF XY: 0.518 AC XY: 38474 AN XY: 74214

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.0325

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.495

Alfa AF: 0.528 Hom.: 42445

Bravo AF: 0.531

Asia WGS AF: 0.269 AC: 935 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.13
DANN	Benign	0.65

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: rs11783247; hg19: chr8-10788875;