rs6982751

chr8-10955964-C-Gchr8-10955964-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.765-31134G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,118 control chromosomes in the GnomAD database, including 3,851 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 0.19 (3851 hom., cov: 33)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XKR6	NM_173683.4	c.765-31134G>C		intron_variant		ENST00000416569.3
XKR6	XM_024447129.2	c.765-31134G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XKR6	ENST00000416569.3	c.765-31134G>C		intron_variant		1	NM_173683.4	P1
XKR6	ENST00000382461.8	c.-13-31134G>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28722 AN: 152000 Hom.: 3843 Cov.: 33

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.0282

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0804

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.189 AC: 28752 AN: 152118 Hom.: 3851 Cov.: 33 AF XY: 0.185 AC XY: 13723 AN XY: 74368

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.0276

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0804

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.166

Alfa AF: 0.0346 Hom.: 33

Bravo AF: 0.199

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.56
Dann	Benign	0.49

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: rs6982751; hg19: chr8-10813474;