rs4240673

Positions:

• chr8-10930102-T-C
• chr8-10930102-T-G

Variant summary

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

The NM_173683.4(XKR6):​c.765-5272A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 152,048 control chromosomes in the GnomAD database, including 24,041 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 (24041 hom., cov: 32)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XKR6	NM_173683.4	c.765-5272A>G		intron_variant		ENST00000416569.3
XKR6	XM_024447129.2	c.765-5272A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XKR6	ENST00000416569.3	c.765-5272A>G		intron_variant		1	NM_173683.4	P1
XKR6	ENST00000382461.8	c.-13-5272A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82084 AN: 151928 Hom.: 24011 Cov.: 32

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.0412

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.540 AC: 82162 AN: 152048 Hom.: 24041 Cov.: 32 AF XY: 0.525 AC XY: 38985 AN XY: 74308

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.0413

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.501

Alfa AF: 0.514 Hom.: 8272

Bravo AF: 0.537

Asia WGS AF: 0.277 AC: 968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.73
DANN	Benign	0.53

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: rs4240673; hg19: chr8-10787612;