rs571623088

Variant names:

• chr3-129421680-C-A
• rs571623088
• NM_207307.3:c.173G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-129421680-C-A
• chr3-129421680-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_207307.3(EFCAB12):​c.173G>T​(p.Arg58Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. R58Q) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: EFCAB12 NM_207307.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.90
• Publications: 4 publications found

Genes affected

EFCAB12 (HGNC:28061): (EF-hand calcium binding domain 12) Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFCAB12	NM_207307.3	c.173G>T	p.Arg58Leu	missense_variant	Exon 2 of 9	ENST00000505956.6	NP_997190.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFCAB12	ENST00000505956.6	c.173G>T	p.Arg58Leu	missense_variant	Exon 2 of 9	1	NM_207307.3	ENSP00000420854.1
EFCAB12	ENST00000503957.1	c.37-3232G>T		intron_variant	Intron 1 of 3	5		ENSP00000421462.1
EFCAB12	ENST00000503498.1	n.-97G>T		upstream_gene_variant		2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.59
BayesDel_addAF	Benign	-0.066	T
BayesDel_noAF	Benign	-0.33
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.024	T;T
Eigen	Benign	0.18
Eigen_PC	Benign	0.10
FATHMM_MKL	Benign	0.49	N
LIST_S2	Benign	0.80	.;T
M_CAP	Benign	0.0072	T
MetaRNN	Uncertain	0.69	D;D
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	2.0	M;M
PhyloP100		2.9
PrimateAI	Benign	0.38	T
PROVEAN	Pathogenic	-5.4	D;D
REVEL	Benign	0.17
Sift	Uncertain	0.012	D;D
Sift4G	Uncertain	0.034	D;D
Polyphen		0.98	D;D
Vest4		0.65
MutPred		0.52		Loss of MoRF binding (P = 0.0218);Loss of MoRF binding (P = 0.0218);
MVP		0.60
MPC		0.38
ClinPred		0.96	D
GERP RS		4.0
Varity_R		0.44
gMVP		0.66
Mutation Taster		=83/17	polymorphism

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: rs571623088; hg19: chr3-129140523;