chr8-55341021-T-C

Variant names:

• chr8-55341021-T-C
• rs1532899
• NM_052898.2:c.807-16657T>C

Variant summary

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

The NM_052898.2(XKR4):​c.807-16657T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 151,988 control chromosomes in the GnomAD database, including 34,967 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 0.67 (34967 hom., cov: 31)
• Consequence: XKR4 NM_052898.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833
• Publications: 3 publications found

Genes affected

XKR4 (HGNC:29394): (XK related 4) Enables phospholipid scramblase activity. Involved in 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052898.2. 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
	XKR4	NM_052898.2	MANE Select	c.807-16657T>C		intron	N/A	NP_443130.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XKR4	ENST00000327381.7	TSL:1 MANE Select	c.807-16657T>C		intron	N/A	ENSP00000328326.5

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101434 AN: 151870 Hom.: 34953 Cov.: 31

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.668 AC: 101478 AN: 151988 Hom.: 34967 Cov.: 31 AF XY: 0.663 AC XY: 49250 AN XY: 74296

African (AFR) AF: 0.500 AC: 20726 AN: 41416

American (AMR) AF: 0.679 AC: 10386 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2286 AN: 3466

East Asian (EAS) AF: 0.513 AC: 2644 AN: 5154

South Asian (SAS) AF: 0.722 AC: 3468 AN: 4806

European-Finnish (FIN) AF: 0.696 AC: 7363 AN: 10574

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52341 AN: 67968

Other (OTH) AF: 0.665 AC: 1405 AN: 2112

Alfa AF: 0.732 Hom.: 184590

Bravo AF: 0.657

Asia WGS AF: 0.608 AC: 2115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.62
PhyloP100		-0.83
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1532899; hg19: chr8-56253581;