rs9349626
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_018100.4(EFHC1):c.573+10A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 1,613,142 control chromosomes in the GnomAD database, including 37,413 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.19 ( 3237 hom., cov: 32)
Exomes 𝑓: 0.21 ( 34176 hom. )
Consequence
EFHC1
NM_018100.4 intron
NM_018100.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.190
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
Variant 6-52438601-A-G is Benign according to our data. Variant chr6-52438601-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 128969.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-52438601-A-G is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFHC1 | NM_018100.4 | c.573+10A>G | intron_variant | ENST00000371068.11 | |||
EFHC1 | NM_001172420.2 | c.516+10A>G | intron_variant | ||||
EFHC1 | NR_033327.2 | n.642+10A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFHC1 | ENST00000371068.11 | c.573+10A>G | intron_variant | 1 | NM_018100.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.191 AC: 28979AN: 151994Hom.: 3229 Cov.: 32
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GnomAD3 exomes AF: 0.237 AC: 59332AN: 250182Hom.: 8565 AF XY: 0.232 AC XY: 31473AN XY: 135484
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GnomAD4 exome AF: 0.208 AC: 303681AN: 1461028Hom.: 34176 Cov.: 35 AF XY: 0.209 AC XY: 151789AN XY: 726852
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GnomAD4 genome ? AF: 0.191 AC: 29000AN: 152114Hom.: 3237 Cov.: 32 AF XY: 0.195 AC XY: 14535AN XY: 74366
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Juvenile myoclonic epilepsy Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 08, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Absence seizure;C1850778:Myoclonic epilepsy, juvenile, susceptibility to, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at