chr8-10955964-C-G

Variant names:

• chr8-10955964-C-G
• rs6982751
• NM_173683.4:c.765-31134G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173683.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XKR6	NM_173683.4	MANE Select	c.765-31134G>C		intron	N/A	NP_775954.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XKR6	ENST00000416569.3	TSL:1 MANE Select	c.765-31134G>C		intron	N/A	ENSP00000416707.2
	XKR6	ENST00000382461.8	TSL:1	c.-13-31134G>C		intron	N/A	ENSP00000371900.4

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

African (AFR) AF: 0.380 AC: 15773 AN: 41464

American (AMR) AF: 0.115 AC: 1751 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 605 AN: 3470

East Asian (EAS) AF: 0.0276 AC: 143 AN: 5174

South Asian (SAS) AF: 0.123 AC: 591 AN: 4824

European-Finnish (FIN) AF: 0.0804 AC: 851 AN: 10590

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8559 AN: 67996

Other (OTH) AF: 0.166 AC: 349 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.49
PhyloP100		-0.85
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6982751; hg19: chr8-10813474;