rs10503417

Positions:

• chr8-11139303-G-A

Variant summary

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

The NM_173683.4(XKR6):​c.764+61273C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,066 control chromosomes in the GnomAD database, including 4,129 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 0.20 (4129 hom., cov: 32)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
XKR6	NM_173683.4	c.764+61273C>T		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+61273C>T		intron_variant		1	NM_173683.4	ENSP00000416707	P1
XKR6	ENST00000529336.1	c.260-25211C>T		intron_variant, NMD_transcript_variant		3		ENSP00000436594

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30391 AN: 151948 Hom.: 4131 Cov.: 32

Gnomad AFR AF: 0.0562

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.200 AC: 30382 AN: 152066 Hom.: 4129 Cov.: 32 AF XY: 0.195 AC XY: 14463 AN XY: 74300

Gnomad4 AFR AF: 0.0560

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.210

Alfa AF: 0.278 Hom.: 3641

Bravo AF: 0.179

Asia WGS AF: 0.0820 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.50

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: rs10503417; hg19: chr8-10996813; COSMIC: COSV69399202; COSMIC: COSV69399202;