rs7460507

chr8-11111565-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+89011G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,860 control chromosomes in the GnomAD database, including 21,887 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 0.50 (21887 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.38

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XKR6	NM_173683.4	c.764+89011G>A		intron_variant		ENST00000416569.3
XKR6	XM_024447129.2	c.764+89011G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XKR6	ENST00000416569.3	c.764+89011G>A		intron_variant		1	NM_173683.4	P1

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76138 AN: 151742 Hom.: 21839 Cov.: 31

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.0598

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.502 AC: 76232 AN: 151860 Hom.: 21887 Cov.: 31 AF XY: 0.490 AC XY: 36331 AN XY: 74190

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.0596

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.448

Alfa AF: 0.447 Hom.: 31715

Bravo AF: 0.507

Asia WGS AF: 0.276 AC: 963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.0020
Dann	Benign	0.19

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: rs7460507; hg19: chr8-10969075;