NM_173683.4:c.764+114810G>A

Variant names:

• chr8-11085766-C-T
• rs2409691
• NM_173683.4:c.764+114810G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173683.4(XKR6):​c.764+114810G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,978 control chromosomes in the GnomAD database, including 21,630 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 0.51 (21630 hom., cov: 31)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 18 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XKR6	NM_173683.4	c.764+114810G>A		intron_variant	Intron 1 of 2	ENST00000416569.3	NP_775954.2
XKR6	XM_024447129.2	c.764+114810G>A		intron_variant	Intron 1 of 2		XP_024302897.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XKR6	ENST00000416569.3	c.764+114810G>A		intron_variant	Intron 1 of 2	1	NM_173683.4	ENSP00000416707.2

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76890 AN: 151860 Hom.: 21603 Cov.: 31

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.0421

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.506 AC: 76953 AN: 151978 Hom.: 21630 Cov.: 31 AF XY: 0.494 AC XY: 36663 AN XY: 74286

African (AFR) AF: 0.720 AC: 29853 AN: 41446

American (AMR) AF: 0.342 AC: 5229 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1722 AN: 3470

East Asian (EAS) AF: 0.0418 AC: 216 AN: 5164

South Asian (SAS) AF: 0.407 AC: 1960 AN: 4818

European-Finnish (FIN) AF: 0.370 AC: 3909 AN: 10566

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32545 AN: 67918

Other (OTH) AF: 0.476 AC: 1006 AN: 2112

Alfa AF: 0.480 Hom.: 56242

Bravo AF: 0.505

Asia WGS AF: 0.236 AC: 825 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	0.0060
DANN	Benign	0.63
PhyloP100		-2.1
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: rs2409691; hg19: chr8-10943276;