8-11198666-A-G

Variant names:

• chr8-11198666-A-G
• rs11783045
• NM_173683.4:c.764+1910T>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.764+1910T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,052 control chromosomes in the GnomAD database, including 7,749 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 0.30 (7749 hom., cov: 31)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XKR6	NM_173683.4	c.764+1910T>C		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+1910T>C		intron_variant	Intron 1 of 2	1	NM_173683.4	ENSP00000416707.2
XKR6	ENST00000297303.4	c.764+1910T>C		intron_variant	Intron 1 of 1	1		ENSP00000297303.4
XKR6	ENST00000529336.1	n.257+1910T>C		intron_variant	Intron 1 of 2	3		ENSP00000436594.1

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46275 AN: 151934 Hom.: 7747 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.304 AC: 46295 AN: 152052 Hom.: 7749 Cov.: 31 AF XY: 0.295 AC XY: 21962 AN XY: 74332

African (AFR) AF: 0.273 AC: 11334 AN: 41448

American (AMR) AF: 0.216 AC: 3300 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1586 AN: 3470

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5178

South Asian (SAS) AF: 0.185 AC: 890 AN: 4818

European-Finnish (FIN) AF: 0.292 AC: 3082 AN: 10556

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25133 AN: 67974

Other (OTH) AF: 0.297 AC: 628 AN: 2112

Alfa AF: 0.309 Hom.: 3252

Bravo AF: 0.294

Asia WGS AF: 0.113 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.75
PhyloP100		0.085
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: rs11783045; hg19: chr8-11056175;