8-55395087-A-C

Variant names:

• chr8-55395087-A-C
• rs2622543
• NM_052898.2:c.1006+37210A>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.1006+37210A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 151,950 control chromosomes in the GnomAD database, including 36,203 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 0.68 (36203 hom., cov: 31)
• Consequence: XKR4 NM_052898.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 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.1006+37210A>C		intron	N/A	NP_443130.1	Q5GH76

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XKR4	ENST00000327381.7	TSL:1 MANE Select	c.1006+37210A>C		intron	N/A	ENSP00000328326.5	Q5GH76

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103407 AN: 151832 Hom.: 36171 Cov.: 31

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.681 AC: 103497 AN: 151950 Hom.: 36203 Cov.: 31 AF XY: 0.679 AC XY: 50401 AN XY: 74234

African (AFR) AF: 0.845 AC: 35035 AN: 41466

American (AMR) AF: 0.618 AC: 9438 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2277 AN: 3466

East Asian (EAS) AF: 0.565 AC: 2895 AN: 5124

South Asian (SAS) AF: 0.651 AC: 3126 AN: 4804

European-Finnish (FIN) AF: 0.571 AC: 6022 AN: 10552

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.625 AC: 42455 AN: 67960

Other (OTH) AF: 0.685 AC: 1444 AN: 2108

Alfa AF: 0.654 Hom.: 4504

Bravo AF: 0.686

Asia WGS AF: 0.609 AC: 2113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.2
DANN	Benign	0.66
PhyloP100		-0.74
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: rs2622543; hg19: chr8-56307647;