rs758521324

Variant names:

• chr13-112690429-C-G
• rs758521324
• NM_015205.3:c.13C>G

Your query was ambiguous. Multiple possible variants found:

• chr13-112690429-C-G
• chr13-112690429-C-T

Variant summary

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

The NM_015205.3(ATP11A):​c.13C>G​(p.Leu5Val) 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. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ATP11A NM_015205.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.847

Genes affected

ATP11A (HGNC:13552): (ATPase phospholipid transporting 11A) The protein encoded by this gene is an integral membrane ATPase. The encoded protein is probably phosphorylated in its intermediate state and likely drives the transport of ions such as calcium across membranes. [provided by RefSeq, Apr 2022]

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=0.12722659).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP11A	NM_015205.3	c.13C>G	p.Leu5Val	missense_variant	Exon 1 of 30	ENST00000375645.8	NP_056020.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP11A	ENST00000375645.8	c.13C>G	p.Leu5Val	missense_variant	Exon 1 of 30	5	NM_015205.3	ENSP00000364796.3
ATP11A	ENST00000375630.6	c.13C>G	p.Leu5Val	missense_variant	Exon 1 of 29	5		ENSP00000364781.2
ATP11A	ENST00000487903.5	c.13C>G	p.Leu5Val	missense_variant	Exon 1 of 30	5		ENSP00000420387.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.057
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.54
CADD	Benign	17
DANN	Uncertain	0.98
DEOGEN2	Benign	0.016	T;T;T
Eigen	Benign	-0.40
Eigen_PC	Benign	-0.24
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Benign	0.67	.;T;T
M_CAP	Pathogenic	0.54	D
MetaRNN	Benign	0.13	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.0	L;L;.
PrimateAI	Uncertain	0.66	T
PROVEAN	Benign	-0.26	N;N;N
REVEL	Benign	0.14
Sift	Benign	0.046	D;D;D
Sift4G	Benign	0.55	T;T;T
Polyphen		0.0080	B;B;B
Vest4		0.25
MutPred		0.58		Gain of catalytic residue at M1 (P = 0);Gain of catalytic residue at M1 (P = 0);Gain of catalytic residue at M1 (P = 0);
MVP		0.26
MPC		0.30
ClinPred		0.093	T
GERP RS		2.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.12
gMVP		0.49

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: rs758521324; hg19: chr13-113344743;