rs7016385

chr8-10921962-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.961+2672G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,006 control chromosomes in the GnomAD database, including 24,292 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 (24292 hom., cov: 32)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XKR6	NM_173683.4	c.961+2672G>A		intron_variant		ENST00000416569.3
XKR6	XM_024447129.2	c.961+2672G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XKR6	ENST00000416569.3	c.961+2672G>A		intron_variant		1	NM_173683.4	P1
XKR6	ENST00000382461.8	c.184+2672G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82479 AN: 151888 Hom.: 24259 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.0392

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.543 AC: 82558 AN: 152006 Hom.: 24292 Cov.: 32 AF XY: 0.528 AC XY: 39276 AN XY: 74316

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.0393

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.506

Alfa AF: 0.545 Hom.: 4005

Bravo AF: 0.541

Asia WGS AF: 0.284 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	2.9
Dann	Benign	0.38

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: rs7016385; hg19: chr8-10779472;