6-52479754-G-C

Variant names:

• chr6-52479754-G-C
• rs867304706
• NM_018100.4:c.1607G>C

Variant summary

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

The NM_018100.4(EFHC1):​c.1607G>C​(p.Arg536Pro) 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. 15/21 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)
• Consequence: EFHC1 NM_018100.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -1.96

Genes affected

EFHC1 (HGNC:16406): (EF-hand domain containing 1) This gene encodes an EF-hand-containing calcium binding protein. The encoded protein likely plays a role in calcium homeostasis. Mutations in this gene have been associated with susceptibility to juvenile myoclonic epilepsy and juvenile absence epilepsy. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2010]

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=0.12849495).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFHC1	NM_018100.4	c.1607G>C	p.Arg536Pro	missense_variant	Exon 9 of 11	ENST00000371068.11	NP_060570.2
EFHC1	NM_001172420.2	c.1550G>C	p.Arg517Pro	missense_variant	Exon 10 of 12		NP_001165891.1
EFHC1	NR_033327.2	n.2933G>C		non_coding_transcript_exon_variant	Exon 8 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFHC1	ENST00000371068.11	c.1607G>C	p.Arg536Pro	missense_variant	Exon 9 of 11	1	NM_018100.4	ENSP00000360107.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Absence seizure;C1850778:Myoclonic epilepsy, juvenile, susceptibility to, 1 Uncertain:1

Oct 17, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces arginine, which is basic and polar, with proline, which is neutral and non-polar, at codon 536 of the EFHC1 protein (p.Arg536Pro). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with EFHC1-related conditions. ClinVar contains an entry for this variant (Variation ID: 571113). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt EFHC1 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Benign	-0.051	T
BayesDel_noAF	Benign	-0.31
CADD	Benign	0.065
DANN	Benign	0.86
DEOGEN2	Benign	0.062	T;.;.;T;T;T;T;T;T;.;T;.;.
Eigen	Benign	-0.91
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.021	N
LIST_S2	Uncertain	0.90	D;D;.;D;D;D;D;D;D;D;D;.;D
M_CAP	Benign	0.016	T
MetaRNN	Benign	0.13	T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.2	.;.;.;M;.;.;.;.;.;.;.;.;.
PrimateAI	Benign	0.22	T
PROVEAN	Benign	-1.4	.;.;.;N;.;.;.;.;.;.;.;.;N
REVEL	Benign	0.23
Sift	Benign	0.26	.;.;.;T;.;.;.;.;.;.;.;.;T
Sift4G	Benign	0.27	.;.;.;T;.;.;.;.;.;.;.;.;T
Polyphen		0.32	.;.;.;B;.;.;.;.;.;.;.;.;.
Vest4		0.49, 0.51
MutPred		0.41		.;.;.;Gain of glycosylation at K537 (P = 0.0547);Gain of glycosylation at K537 (P = 0.0547);Gain of glycosylation at K537 (P = 0.0547);Gain of glycosylation at K537 (P = 0.0547);Gain of glycosylation at K537 (P = 0.0547);.;Gain of glycosylation at K537 (P = 0.0547);.;.;.;
MVP		0.69
MPC		0.17
ClinPred		0.12	T
GERP RS		-3.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.16
gMVP		0.66

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: rs867304706; hg19: chr6-52344552;