rs201860746
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_018100.4(EFHC1):c.64-5T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00084 in 1,613,990 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_018100.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFHC1 | NM_018100.4 | c.64-5T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000371068.11 | |||
EFHC1 | NM_001172420.2 | c.7-5T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
EFHC1 | NR_033327.2 | n.133-5T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFHC1 | ENST00000371068.11 | c.64-5T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_018100.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000585 AC: 89AN: 152168Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000868 AC: 218AN: 251086Hom.: 0 AF XY: 0.000891 AC XY: 121AN XY: 135814
GnomAD4 exome AF: 0.000867 AC: 1267AN: 1461822Hom.: 1 Cov.: 32 AF XY: 0.000887 AC XY: 645AN XY: 727222
GnomAD4 genome ? AF: 0.000585 AC: 89AN: 152168Hom.: 1 Cov.: 32 AF XY: 0.000605 AC XY: 45AN XY: 74340
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 02, 2014 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 28, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 31, 2017 | - - |
Juvenile myoclonic epilepsy Uncertain:1
Uncertain significance, 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 | Jul 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at