rs10504490

chr8-70962830-C-T

Variant summary

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

The XM_011517527.4(XKR9):c.494-102527C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0596 in 152,256 control chromosomes in the GnomAD database, including 382 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 0.060 (382 hom., cov: 32)
• Consequence: XKR9 XM_011517527.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

Genes affected

XKR9 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
XKR9	XM_011517527.4	c.494-102527C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9068 AN: 152138 Hom.: 380 Cov.: 32

Gnomad AFR AF: 0.0256

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0516

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0358

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0844

Gnomad OTH AF: 0.0757

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

GnomAD4 genome AF: 0.0596 AC: 9072 AN: 152256 Hom.: 382 Cov.: 32 AF XY: 0.0570 AC XY: 4241 AN XY: 74450

Gnomad4 AFR AF: 0.0255

Gnomad4 AMR AF: 0.0515

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0373

Gnomad4 FIN AF: 0.0520

Gnomad4 NFE AF: 0.0844

Gnomad4 OTH AF: 0.0744

Alfa AF: 0.0693 Hom.: 53

Bravo AF: 0.0583

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.4
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504490; hg19: chr8-71875065;