8-11139157-A-G

Position:

• chr8-11139157-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173683.4(XKR6):​c.764+61419T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,292 control chromosomes in the GnomAD database, including 3,177 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 0.14 (3177 hom., cov: 33)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
XKR6	NM_173683.4	c.764+61419T>C		intron_variant		ENST00000416569.3	NP_775954.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
XKR6	ENST00000416569.3	c.764+61419T>C		intron_variant		1	NM_173683.4	ENSP00000416707	P1
XKR6	ENST00000529336.1	c.260-25065T>C		intron_variant, NMD_transcript_variant		3		ENSP00000436594

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21280 AN: 152174 Hom.: 3168 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0925

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.0148

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0146

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0418

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.140 AC: 21313 AN: 152292 Hom.: 3177 Cov.: 33 AF XY: 0.136 AC XY: 10133 AN XY: 74480

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.0923

Gnomad4 ASJ AF: 0.0703

Gnomad4 EAS AF: 0.0148

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0146

Gnomad4 NFE AF: 0.0418

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0705 Hom.: 422

Bravo AF: 0.154

Asia WGS AF: 0.0780 AC: 270 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	8.1
DANN	Benign	0.69

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: rs10282848; hg19: chr8-10996667;