6-52424047-C-A

Position:

• chr6-52424047-C-A

Variant summary

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

The NM_018100.4(EFHC1):​c.165C>A​(p.Asn55Lys) 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.

• Frequency: Genomes: not found (cov: 32)
• Consequence: EFHC1 NM_018100.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520

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=0.18371376).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EFHC1	NM_018100.4	c.165C>A	p.Asn55Lys	missense_variant	2/11	ENST00000371068.11	NP_060570.2
EFHC1	NM_001172420.2	c.108C>A	p.Asn36Lys	missense_variant	3/12		NP_001165891.1
EFHC1	NR_033327.2	n.234C>A		non_coding_transcript_exon_variant	2/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFHC1	ENST00000371068.11	c.165C>A	p.Asn55Lys	missense_variant	2/11	1	NM_018100.4	ENSP00000360107	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.43
CADD	Benign	18
DANN	Uncertain	0.98
DEOGEN2	Benign	0.31	.;.;T;T;T;T;T;T;.;T;.;.
Eigen	Benign	-0.47
Eigen_PC	Benign	-0.31
FATHMM_MKL	Benign	0.44	N
LIST_S2	Benign	0.78	T;.;T;T;T;T;T;T;T;T;.;T
M_CAP	Benign	0.020	T
MetaRNN	Benign	0.18	T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	2.0	.;.;M;.;.;.;.;.;.;.;.;.
MutationTaster	Benign	0.99	D;D;D
PrimateAI	Benign	0.40	T
PROVEAN	Uncertain	-3.5	.;.;D;.;.;.;.;.;.;.;.;D
REVEL	Benign	0.11
Sift	Benign	0.13	.;.;T;.;.;.;.;.;.;.;.;T
Sift4G	Benign	0.33	.;.;T;.;.;.;.;.;.;.;.;T
Polyphen		0.0010	.;.;B;.;.;.;.;.;.;.;.;.
Vest4		0.23, 0.19
MutPred		0.47		.;.;Gain of ubiquitination at N55 (P = 0.0077);Gain of ubiquitination at N55 (P = 0.0077);Gain of ubiquitination at N55 (P = 0.0077);Gain of ubiquitination at N55 (P = 0.0077);Gain of ubiquitination at N55 (P = 0.0077);.;Gain of ubiquitination at N55 (P = 0.0077);Gain of ubiquitination at N55 (P = 0.0077);.;.;
MVP		0.70
MPC		0.10
ClinPred		0.68	D
GERP RS		4.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.13
gMVP		0.40

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: rs928396576; hg19: chr6-52288845;