rs10504485

chr8-70911467-G-A

Variant summary

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

The XM_011517527.4(XKR9):c.494-153890G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0838 in 152,206 control chromosomes in the GnomAD database, including 609 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 0.084 (609 hom., cov: 32)
• Consequence: XKR9 XM_011517527.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

Genes affected

XKR9 (HGNC:):

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 = 0.0946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XKR9	XM_011517527.4	c.494-153890G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0838 AC: 12742 AN: 152088 Hom.: 605 Cov.: 32

Gnomad AFR AF: 0.0971

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0621

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0389

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.0838 AC: 12755 AN: 152206 Hom.: 609 Cov.: 32 AF XY: 0.0807 AC XY: 6005 AN XY: 74400

Gnomad4 AFR AF: 0.0971

Gnomad4 AMR AF: 0.0619

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0404

Gnomad4 FIN AF: 0.0603

Gnomad4 NFE AF: 0.0896

Gnomad4 OTH AF: 0.0899

Alfa AF: 0.0859 Hom.: 78

Bravo AF: 0.0844

Asia WGS AF: 0.0160 AC: 57 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.14
Dann	Benign	0.37

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10504485; hg19: chr8-71823702;