rs10101292

Positions:

• chr8-10998964-T-C

Variant summary

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

The NM_173683.4(XKR6):​c.765-74134A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,122 control chromosomes in the GnomAD database, including 10,236 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 0.35 (10236 hom., cov: 33)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XKR6	NM_173683.4	c.765-74134A>G		intron_variant		ENST00000416569.3
XKR6	XM_024447129.2	c.765-74134A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XKR6	ENST00000416569.3	c.765-74134A>G		intron_variant		1	NM_173683.4	P1
XKR6	ENST00000382461.8	c.-14+3424A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53988 AN: 152006 Hom.: 10238 Cov.: 33

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.0158

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.355 AC: 53986 AN: 152122 Hom.: 10236 Cov.: 33 AF XY: 0.345 AC XY: 25677 AN XY: 74382

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.0158

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.348

Alfa AF: 0.380 Hom.: 3575

Bravo AF: 0.343

Asia WGS AF: 0.198 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.56
DANN	Benign	0.46

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: rs10101292; hg19: chr8-10856474;