rs10101292

Variant names:

• chr8-10998964-T-C
• rs10101292
• NM_173683.4:c.765-74134A>G

Variant summary

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

The ENST00000416569.3(XKR6):​c.765-74134A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,122 control chromosomes in the GnomAD database, including 10,236 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 0.35 (10236 hom., cov: 33)
• Consequence: XKR6 ENST00000416569.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416569.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XKR6	NM_173683.4	MANE Select	c.765-74134A>G		intron	N/A	NP_775954.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XKR6	ENST00000416569.3	TSL:1 MANE Select	c.765-74134A>G		intron	N/A	ENSP00000416707.2
	XKR6	ENST00000382461.8	TSL:1	c.-14+3424A>G		intron	N/A	ENSP00000371900.4

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53988 AN: 152006 Hom.: 10238 Cov.: 33

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.0158

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.355 AC: 53986 AN: 152122 Hom.: 10236 Cov.: 33 AF XY: 0.345 AC XY: 25677 AN XY: 74382

African (AFR) AF: 0.335 AC: 13885 AN: 41492

American (AMR) AF: 0.243 AC: 3721 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1562 AN: 3470

East Asian (EAS) AF: 0.0158 AC: 82 AN: 5184

South Asian (SAS) AF: 0.346 AC: 1666 AN: 4818

European-Finnish (FIN) AF: 0.315 AC: 3336 AN: 10580

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28540 AN: 67974

Other (OTH) AF: 0.348 AC: 736 AN: 2112

Alfa AF: 0.381 Hom.: 4442

Bravo AF: 0.343

Asia WGS AF: 0.198 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.56
DANN	Benign	0.46
PhyloP100		-0.68
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: rs10101292; hg19: chr8-10856474;