8-11155467-C-T

Variant names:

• chr8-11155467-C-T
• rs2409718
• NM_173683.4:c.764+45109G>A

Variant summary

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

The NM_173683.4(XKR6):​c.764+45109G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,130 control chromosomes in the GnomAD database, including 28,884 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 0.58 (28884 hom., cov: 33)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

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 = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XKR6	NM_173683.4	c.764+45109G>A		intron_variant	Intron 1 of 2	ENST00000416569.3	NP_775954.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XKR6	ENST00000416569.3	c.764+45109G>A		intron_variant	Intron 1 of 2	1	NM_173683.4	ENSP00000416707.2
XKR6	ENST00000529336.1	n.258-41375G>A		intron_variant	Intron 1 of 2	3		ENSP00000436594.1

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87887 AN: 152012 Hom.: 28833 Cov.: 33

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.0654

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.578 AC: 87982 AN: 152130 Hom.: 28884 Cov.: 33 AF XY: 0.563 AC XY: 41905 AN XY: 74372

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.0652

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.543

Alfa AF: 0.515 Hom.: 40791

Bravo AF: 0.585

Asia WGS AF: 0.296 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.013
DANN	Benign	0.21

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: rs2409718; hg19: chr8-11012977;