rs4326350

chr8-10906145-C-G

Variant summary

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

The NM_173683.4(XKR6):c.962-7229G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,050 control chromosomes in the GnomAD database, including 19,067 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 0.48 (19067 hom., cov: 33)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XKR6	NM_173683.4	c.962-7229G>C		intron_variant		ENST00000416569.3
XKR6	XM_024447129.2	c.962-7130G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
XKR6	ENST00000416569.3	c.962-7229G>C		intron_variant		1	NM_173683.4	P1
XKR6	ENST00000382461.8	c.185-7229G>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73366 AN: 151932 Hom.: 19045 Cov.: 33

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.0217

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.483 AC: 73425 AN: 152050 Hom.: 19067 Cov.: 33 AF XY: 0.471 AC XY: 35026 AN XY: 74344

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.0218

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.457

Alfa AF: 0.511 Hom.: 2550

Bravo AF: 0.483

Asia WGS AF: 0.255 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.0
Dann	Benign	0.35

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: rs4326350; hg19: chr8-10763655;