rs10504489

chr8-70945275-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XM_011517527.4(XKR9):c.494-120082T>C 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 152,242 control chromosomes in the GnomAD database, including 381 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 (381 hom., cov: 32)
• Consequence: XKR9 XM_011517527.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.638

Genes affected

XKR9 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• 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.494-120082T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9063 AN: 152122 Hom.: 379 Cov.: 32

Gnomad AFR AF: 0.0256

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0517

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0354

Gnomad FIN AF: 0.0519

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.0843

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: 9067 AN: 152242 Hom.: 381 Cov.: 32 AF XY: 0.0569 AC XY: 4237 AN XY: 74442

Gnomad4 AFR AF: 0.0256

Gnomad4 AMR AF: 0.0516

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0369

Gnomad4 FIN AF: 0.0519

Gnomad4 NFE AF: 0.0843

Gnomad4 OTH AF: 0.0745

Alfa AF: 0.0770 Hom.: 241

Bravo AF: 0.0582

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	-0.30
Cadd	Benign	14
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504489; hg19: chr8-71857510;