rs2001433

Positions:

• chr8-11045965-T-A
• chr8-11045965-T-C

Variant summary

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

The NM_173683.4(XKR6):​c.765-121135A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 152,174 control chromosomes in the GnomAD database, including 29,174 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 0.58 (29174 hom., cov: 33)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
XKR6	NM_173683.4	c.765-121135A>T		intron_variant		ENST00000416569.3	NP_775954.2
XKR6	XM_024447129.2	c.765-121135A>T		intron_variant			XP_024302897.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
XKR6	ENST00000416569.3	c.765-121135A>T		intron_variant		1	NM_173683.4	ENSP00000416707	P1

Frequencies

GnomAD3 genomes AF: 0.579 AC: 88011 AN: 152056 Hom.: 29115 Cov.: 33

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.0300

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.579 AC: 88110 AN: 152174 Hom.: 29174 Cov.: 33 AF XY: 0.564 AC XY: 41957 AN XY: 74386

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.0297

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.534

Alfa AF: 0.433 Hom.: 1061

Bravo AF: 0.583

Asia WGS AF: 0.276 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.82

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: rs2001433; hg19: chr8-10903475;