chr6-52420216-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000637340.1(EFHC1):n.474A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0299 in 758,872 control chromosomes in the GnomAD database, including 890 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.043 ( 243 hom., cov: 32)
Exomes 𝑓: 0.026 ( 647 hom. )
Consequence
EFHC1
ENST00000637340.1 non_coding_transcript_exon
ENST00000637340.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.279
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=-0.78).
BP6
?
Variant 6-52420216-A-G is Benign according to our data. Variant chr6-52420216-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 357475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC124901331 | XR_007059611.1 | n.766T>C | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFHC1 | ENST00000637340.1 | n.474A>G | non_coding_transcript_exon_variant | 1/10 | 1 | ||||
EFHC1 | ENST00000636489.1 | c.-380A>G | 5_prime_UTR_variant | 1/12 | 5 | ||||
EFHC1 | ENST00000635760.1 | c.-261-3730A>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0433 AC: 6585AN: 152188Hom.: 241 Cov.: 32
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GnomAD3 exomes AF: 0.0290 AC: 4108AN: 141872Hom.: 188 AF XY: 0.0271 AC XY: 2059AN XY: 76070
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GnomAD4 exome AF: 0.0265 AC: 16065AN: 606566Hom.: 647 Cov.: 7 AF XY: 0.0252 AC XY: 8171AN XY: 324886
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GnomAD4 genome ? AF: 0.0434 AC: 6603AN: 152306Hom.: 243 Cov.: 32 AF XY: 0.0439 AC XY: 3271AN XY: 74474
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Juvenile myoclonic epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 20, 2019 | - - |
Computational scores
Source:
Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at