chr2-232648465-C-G

Variant names:

• chr2-232648465-C-G
• rs2140773
• NM_025202.4:c.303-14337C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_025202.4(EFHD1):​c.303-14337C>G variant causes a intron 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: EFHD1 NM_025202.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 22 publications found

Genes affected

EFHD1 (HGNC:29556): (EF-hand domain family member D1) This gene encodes a member of the EF-hand super family of calcium binding proteins, which are involved in a variety of cellular processes including mitosis, synaptic transmission, and cytoskeletal rearrangement. The protein encoded by this gene is composed of an N-terminal disordered region, proline-rich elements, two EF-hands, and a C-terminal coiled-coil domain. This protein has been shown to associate with the mitochondrial inner membrane, and in HeLa cells, acts as a novel mitochondrial calcium ion sensor for mitochondrial flash activation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFHD1	NM_025202.4	c.303-14337C>G		intron_variant	Intron 1 of 3	ENST00000264059.8	NP_079478.1
EFHD1	NM_001243252.2	c.15-14337C>G		intron_variant	Intron 1 of 3		NP_001230181.1
EFHD1	NM_001308395.2	c.-35+9981C>G		intron_variant	Intron 2 of 4		NP_001295324.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFHD1	ENST00000264059.8	c.303-14337C>G		intron_variant	Intron 1 of 3	1	NM_025202.4	ENSP00000264059.3
EFHD1	ENST00000409613.5	c.15-14337C>G		intron_variant	Intron 1 of 3	1		ENSP00000386556.1
EFHD1	ENST00000409708.5	c.-35+9981C>G		intron_variant	Intron 1 of 3	2		ENSP00000386243.1
EFHD1	ENST00000442845.1	n.*72+9981C>G		intron_variant	Intron 2 of 4	3		ENSP00000395119.1

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.068
DANN	Benign	0.19
PhyloP100		-1.3

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: rs2140773; hg19: chr2-233513175;