NM_173683.4:c.962-5159C>T

Variant names:

• chr8-10904075-G-A
• rs6985109
• NM_173683.4:c.962-5159C>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.962-5159C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,982 control chromosomes in the GnomAD database, including 22,867 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 0.53 (22867 hom., cov: 32)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 34 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173683.4. 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.962-5159C>T		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.962-5159C>T		intron	N/A	ENSP00000416707.2
	XKR6	ENST00000382461.8	TSL:1	c.185-5159C>T		intron	N/A	ENSP00000371900.4

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80082 AN: 151862 Hom.: 22840 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.0314

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.527 AC: 80151 AN: 151982 Hom.: 22867 Cov.: 32 AF XY: 0.512 AC XY: 38045 AN XY: 74268

African (AFR) AF: 0.692 AC: 28694 AN: 41452

American (AMR) AF: 0.374 AC: 5715 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2031 AN: 3468

East Asian (EAS) AF: 0.0315 AC: 163 AN: 5180

South Asian (SAS) AF: 0.402 AC: 1928 AN: 4800

European-Finnish (FIN) AF: 0.387 AC: 4079 AN: 10538

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35975 AN: 67946

Other (OTH) AF: 0.495 AC: 1048 AN: 2116

Alfa AF: 0.518 Hom.: 67234

Bravo AF: 0.528

Asia WGS AF: 0.267 AC: 930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.7
DANN	Benign	0.79
PhyloP100		0.23
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: rs6985109; hg19: chr8-10761585;