rs17782554

Variant names:

• chr8-11164596-G-C
• rs17782554
• NM_173683.4:c.764+35980C>G

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+35980C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,124 control chromosomes in the GnomAD database, including 7,298 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 0.28 (7298 hom., cov: 33)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.479
• Publications: 11 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.387 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.764+35980C>G		intron	N/A	NP_775954.2
	XKR6	NR_138152.2		n.1389+30495C>G		intron	N/A
	XKR6	NR_138153.2		n.1258+35980C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XKR6	ENST00000416569.3	TSL:1 MANE Select	c.764+35980C>G		intron	N/A	ENSP00000416707.2
	XKR6	ENST00000529336.1	TSL:3	n.257+35980C>G		intron	N/A	ENSP00000436594.1

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42782 AN: 152006 Hom.: 7299 Cov.: 33

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.281 AC: 42775 AN: 152124 Hom.: 7298 Cov.: 33 AF XY: 0.274 AC XY: 20368 AN XY: 74362

African (AFR) AF: 0.140 AC: 5820 AN: 41488

American (AMR) AF: 0.209 AC: 3201 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1604 AN: 3470

East Asian (EAS) AF: 0.00386 AC: 20 AN: 5184

South Asian (SAS) AF: 0.202 AC: 974 AN: 4828

European-Finnish (FIN) AF: 0.341 AC: 3607 AN: 10570

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26550 AN: 67978

Other (OTH) AF: 0.298 AC: 628 AN: 2110

Alfa AF: 0.360 Hom.: 1386

Bravo AF: 0.262

Asia WGS AF: 0.106 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.76
PhyloP100		0.48
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: rs17782554; hg19: chr8-11022106;