chr8-55404181-C-G

Variant names:

• chr8-55404181-C-G
• rs2622542
• NM_052898.2:c.1006+46304C>G

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+46304C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 152,020 control chromosomes in the GnomAD database, including 39,758 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 0.71 (39758 hom., cov: 32)
• Consequence: XKR4 NM_052898.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 4 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 = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XKR4	NM_052898.2	c.1006+46304C>G		intron_variant	Intron 2 of 2	ENST00000327381.7	NP_443130.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XKR4	ENST00000327381.7	c.1006+46304C>G		intron_variant	Intron 2 of 2	1	NM_052898.2	ENSP00000328326.5

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108288 AN: 151902 Hom.: 39711 Cov.: 32

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.713 AC: 108396 AN: 152020 Hom.: 39758 Cov.: 32 AF XY: 0.711 AC XY: 52781 AN XY: 74276

African (AFR) AF: 0.891 AC: 36991 AN: 41502

American (AMR) AF: 0.637 AC: 9721 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2349 AN: 3466

East Asian (EAS) AF: 0.566 AC: 2928 AN: 5176

South Asian (SAS) AF: 0.681 AC: 3278 AN: 4810

European-Finnish (FIN) AF: 0.596 AC: 6277 AN: 10526

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44511 AN: 67968

Other (OTH) AF: 0.712 AC: 1499 AN: 2106

Alfa AF: 0.697 Hom.: 4672

Bravo AF: 0.718

Asia WGS AF: 0.631 AC: 2192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.9
DANN	Benign	0.32
PhyloP100		0.043
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: rs2622542; hg19: chr8-56316741;