8-70993352-T-G

Variant names:

• chr8-70993352-T-G
• rs1493202
• XM_011517527.4:c.494-72005T>G

Variant summary

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

The ENST00000647843.1(ENSG00000285579):​n.328-60125T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,940 control chromosomes in the GnomAD database, including 14,224 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 0.41 (14224 hom., cov: 31)
• Consequence: ENSG00000285579 ENST00000647843.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 12 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.541 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.328-60125T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62051 AN: 151824 Hom.: 14210 Cov.: 31

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.408 AC: 62066 AN: 151940 Hom.: 14224 Cov.: 31 AF XY: 0.410 AC XY: 30412 AN XY: 74254

African (AFR) AF: 0.192 AC: 7941 AN: 41440

American (AMR) AF: 0.551 AC: 8421 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1251 AN: 3468

East Asian (EAS) AF: 0.337 AC: 1735 AN: 5142

South Asian (SAS) AF: 0.302 AC: 1455 AN: 4814

European-Finnish (FIN) AF: 0.507 AC: 5347 AN: 10554

Middle Eastern (MID) AF: 0.455 AC: 132 AN: 290

European-Non Finnish (NFE) AF: 0.505 AC: 34332 AN: 67946

Other (OTH) AF: 0.420 AC: 881 AN: 2096

Alfa AF: 0.432 Hom.: 15679

Bravo AF: 0.407

Asia WGS AF: 0.336 AC: 1172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.95
DANN	Benign	0.60
PhyloP100		-0.19

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: rs1493202;

hg19: chr8-71905587;