rs200806311

Variant names:

• chr8-70707139-C-A
• rs200806311
• NM_001011720.2:c.479C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-70707139-C-A
• chr8-70707139-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001011720.2(XKR9):​c.479C>A​(p.Ala160Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A160V) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: XKR9 NM_001011720.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.25623193).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XKR9	NM_001011720.2	c.479C>A	p.Ala160Glu	missense_variant	Exon 4 of 5	ENST00000408926.8	NP_001011720.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XKR9	ENST00000408926.8	c.479C>A	p.Ala160Glu	missense_variant	Exon 4 of 5	1	NM_001011720.2	ENSP00000386141.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.17	T
BayesDel_noAF	Benign	-0.49
CADD	Benign	3.7
DANN	Benign	0.87
DEOGEN2	Benign	0.061	T;T
Eigen	Benign	-0.71
Eigen_PC	Benign	-0.91
FATHMM_MKL	Benign	0.031	N
LIST_S2	Benign	0.48	.;T
M_CAP	Benign	0.031	D
MetaRNN	Benign	0.26	T;T
MetaSVM	Benign	-0.90	T
MutationAssessor	Uncertain	2.7	M;M
PrimateAI	Benign	0.26	T
PROVEAN	Uncertain	-2.7	D;D
REVEL	Benign	0.20
Sift	Benign	0.51	T;T
Sift4G	Benign	0.46	T;T
Polyphen		0.83	P;P
Vest4		0.28
MutPred		0.72		Gain of solvent accessibility (P = 0.0068);Gain of solvent accessibility (P = 0.0068);
MVP		0.52
MPC		0.0021
ClinPred		0.35	T
GERP RS		-2.5
Varity_R		0.20
gMVP		0.33

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

Publications

LitVar

Other links and lift over

dbSNP: rs200806311; hg19: chr8-71619374;