rs10504486

Variant names:

• chr8-70931346-A-G
• rs10504486
• XM_011517527.4:c.494-134011A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647843.1(ENSG00000285579):​n.328-122131A>G 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 152,180 control chromosomes in the GnomAD database, including 383 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 (383 hom., cov: 32)
• Consequence: ENSG00000285579 ENST00000647843.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763
• Publications: 1 publications found

Genes affected

XKR9 (HGNC:20937): (XK related 9) Predicted to enable phospholipid scramblase activity. 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]

ENSG00000285579 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0825 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647843.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285579	ENST00000647843.1		n.328-122131A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9060 AN: 152062 Hom.: 381 Cov.: 32

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0516

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0352

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: 9064 AN: 152180 Hom.: 383 Cov.: 32 AF XY: 0.0569 AC XY: 4236 AN XY: 74414

African (AFR) AF: 0.0255 AC: 1059 AN: 41534

American (AMR) AF: 0.0515 AC: 786 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 515 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5172

South Asian (SAS) AF: 0.0367 AC: 177 AN: 4820

European-Finnish (FIN) AF: 0.0520 AC: 552 AN: 10606

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0844 AC: 5735 AN: 67990

Other (OTH) AF: 0.0745 AC: 157 AN: 2108

Alfa AF: 0.0682 Hom.: 55

Bravo AF: 0.0582

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.23
DANN	Benign	0.60
PhyloP100		-0.76

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10504486;

hg19: chr8-71843581;