rs2001329

Positions:

• chr8-11129349-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.764+71227G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 151,854 control chromosomes in the GnomAD database, including 24,901 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 0.54 (24901 hom., cov: 33)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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 = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
XKR6	NM_173683.4	c.764+71227G>A		intron_variant		ENST00000416569.3	NP_775954.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
XKR6	ENST00000416569.3	c.764+71227G>A		intron_variant		1	NM_173683.4	ENSP00000416707	P1
XKR6	ENST00000529336.1	c.260-15257G>A		intron_variant, NMD_transcript_variant		3		ENSP00000436594

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82516 AN: 151736 Hom.: 24883 Cov.: 33

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.544 AC: 82574 AN: 151854 Hom.: 24901 Cov.: 33 AF XY: 0.530 AC XY: 39327 AN XY: 74208

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.0341

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.510

Alfa AF: 0.562 Hom.: 3752

Bravo AF: 0.546

Asia WGS AF: 0.253 AC: 884 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	0.28
DANN	Benign	0.40

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: rs2001329; hg19: chr8-10986859;