chr8-11159379-A-G

Variant names:

• chr8-11159379-A-G
• rs2409719
• NM_173683.4:c.764+41197T>C

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+41197T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,146 control chromosomes in the GnomAD database, including 7,273 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 (7273 hom., cov: 33)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XKR6	NM_173683.4	c.764+41197T>C		intron_variant	Intron 1 of 2	ENST00000416569.3	NP_775954.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XKR6	ENST00000416569.3	c.764+41197T>C		intron_variant	Intron 1 of 2	1	NM_173683.4	ENSP00000416707.2
XKR6	ENST00000529336.1	n.257+41197T>C		intron_variant	Intron 1 of 2	3		ENSP00000436594.1

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43208 AN: 152028 Hom.: 7271 Cov.: 33

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.284 AC: 43223 AN: 152146 Hom.: 7273 Cov.: 33 AF XY: 0.277 AC XY: 20571 AN XY: 74396

African (AFR) AF: 0.163 AC: 6770 AN: 41518

American (AMR) AF: 0.209 AC: 3188 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1605 AN: 3460

East Asian (EAS) AF: 0.00405 AC: 21 AN: 5186

South Asian (SAS) AF: 0.183 AC: 884 AN: 4824

European-Finnish (FIN) AF: 0.339 AC: 3587 AN: 10572

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26166 AN: 67976

Other (OTH) AF: 0.299 AC: 632 AN: 2114

Alfa AF: 0.341 Hom.: 5116

Bravo AF: 0.266

Asia WGS AF: 0.101 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.8
DANN	Benign	0.77
PhyloP100		-1.6
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: rs2409719; hg19: chr8-11016889;