rs775583843
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PVS1_ModerateBP6_ModerateBS2
The ENST00000371068.11(EFHC1):c.1841_1851+13del variant causes a splice donor, splice donor 5th base, coding sequence, intron change. The variant allele was found at a frequency of 0.0000675 in 1,613,952 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000072 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000067 ( 0 hom. )
Consequence
EFHC1
ENST00000371068.11 splice_donor, splice_donor_5th_base, coding_sequence, intron
ENST00000371068.11 splice_donor, splice_donor_5th_base, coding_sequence, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.70
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PVS1
Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates 0.0431617264690588 fraction of the geneNo cryptic splice site detected. Exon removal results in frameshift change.
BP6
Variant 6-52490338-CTTGGTTAAGGAGGTCAGTATGAAT-C is Benign according to our data. Variant chr6-52490338-CTTGGTTAAGGAGGTCAGTATGAAT-C is described in ClinVar as [Likely_benign]. Clinvar id is 411576.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 11 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EFHC1 | NM_018100.4 | c.1841_1851+13del | splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant | 10/11 | ENST00000371068.11 | NP_060570.2 | ||
EFHC1 | NM_001172420.2 | c.1784_1794+13del | splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant | 11/12 | NP_001165891.1 | |||
EFHC1 | NR_033327.2 | n.3167_3177+13del | splice_donor_variant, splice_donor_5th_base_variant, non_coding_transcript_exon_variant, intron_variant | 9/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EFHC1 | ENST00000371068.11 | c.1841_1851+13del | splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant | 10/11 | 1 | NM_018100.4 | ENSP00000360107 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152148Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
11
AN:
152148
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000917 AC: 23AN: 250924Hom.: 0 AF XY: 0.0000959 AC XY: 13AN XY: 135618
GnomAD3 exomes
AF:
AC:
23
AN:
250924
Hom.:
AF XY:
AC XY:
13
AN XY:
135618
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000670 AC: 98AN: 1461686Hom.: 0 AF XY: 0.0000633 AC XY: 46AN XY: 727148
GnomAD4 exome
AF:
AC:
98
AN:
1461686
Hom.:
AF XY:
AC XY:
46
AN XY:
727148
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74446
GnomAD4 genome
AF:
AC:
11
AN:
152266
Hom.:
Cov.:
32
AF XY:
AC XY:
4
AN XY:
74446
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Absence seizure;C1850778:Myoclonic epilepsy, juvenile, susceptibility to, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 23, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at