Variant 3-129418345-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_207307.3(EFCAB12):c.590G>T(p.Arg197Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,461,482 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000041 ( 0 hom. )

Consequence

EFCAB12
NM_207307.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.64

Variant links:

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]

EFCAB12 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.27930683).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EFCAB12	NM_207307.3 linkuse as main transcript	c.590G>T	p.Arg197Leu	missense_variant	3/9	ENST00000505956.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
EFCAB12	ENST00000505956.6 linkuse as main transcript	c.590G>T	p.Arg197Leu	missense_variant	3/9	1	NM_207307.3	P1
EFCAB12	ENST00000503957.1 linkuse as main transcript	c.140G>T	p.Arg47Leu	missense_variant	2/4	5
EFCAB12	ENST00000503498.1 linkuse as main transcript	n.321G>T		non_coding_transcript_exon_variant	2/7	2
EFCAB12	ENST00000514900.5 linkuse as main transcript	n.179G>T		non_coding_transcript_exon_variant	1/6	2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000411

AC:

AN:

1461482

Hom.:

Cov.:

AF XY:

0.00000688

AC XY:

AN XY:

727014

show subpopulations

Gnomad4 AFR exome

AF:

0.0000299

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

8.99e-7

Gnomad4 OTH exome

AF:

0.0000497

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.29

BayesDel_addAF

Benign

-0.12

BayesDel_noAF

Benign

-0.41

CADD

Benign

8.7

DANN

Uncertain

0.99

DEOGEN2

Benign

0.045

T;T;.

Eigen

Benign

-0.63

Eigen_PC

Benign

-0.86

FATHMM_MKL

Benign

0.21

M_CAP

Benign

0.019

MetaRNN

Benign

0.28

T;T;T

MetaSVM

Benign

-0.94

MutationAssessor

Uncertain

2.2

M;M;.

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.25

PROVEAN

Pathogenic

-5.4

D;D;D

REVEL

Benign

0.14

Sift

Uncertain

0.011

D;D;D

Sift4G

Uncertain

0.014

D;D;.

Polyphen

0.96

D;D;.

Vest4

0.49

MutPred

0.41

Loss of sheet (P = 0.0142);Loss of sheet (P = 0.0142);.;

MVP

0.31

MPC

0.38

ClinPred

0.95

GERP RS

-3.3

Varity_R

0.15

gMVP

0.45

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

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over