rs13266785

Variant names:

• chr8-11132011-G-A
• rs13266785
• NM_173683.4:c.764+68565C>T

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+68565C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,916 control chromosomes in the GnomAD database, including 10,554 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 0.36 (10554 hom., cov: 32)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• Publications: 10 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XKR6	NM_173683.4	c.764+68565C>T		intron_variant	Intron 1 of 2	ENST00000416569.3	NP_775954.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XKR6	ENST00000416569.3	c.764+68565C>T		intron_variant	Intron 1 of 2	1	NM_173683.4	ENSP00000416707.2
XKR6	ENST00000529336.1	n.258-17919C>T		intron_variant	Intron 1 of 2	3		ENSP00000436594.1

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54336 AN: 151798 Hom.: 10553 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.358 AC: 54355 AN: 151916 Hom.: 10554 Cov.: 32 AF XY: 0.347 AC XY: 25743 AN XY: 74290

African (AFR) AF: 0.429 AC: 17730 AN: 41336

American (AMR) AF: 0.242 AC: 3697 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1610 AN: 3468

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5182

South Asian (SAS) AF: 0.183 AC: 879 AN: 4814

European-Finnish (FIN) AF: 0.330 AC: 3490 AN: 10570

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25847 AN: 67952

Other (OTH) AF: 0.338 AC: 712 AN: 2108

Alfa AF: 0.374 Hom.: 5722

Bravo AF: 0.350

Asia WGS AF: 0.112 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.37
PhyloP100		-0.20
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: rs13266785; hg19: chr8-10989521;