chrX-44248815-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_025184.4(EFHC2):c.960C>T(p.Phe320=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000747 in 1,204,477 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 38 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000054 ( 0 hom., 4 hem., cov: 23)
Exomes 𝑓: 0.000077 ( 0 hom. 34 hem. )
Consequence
EFHC2
NM_025184.4 synonymous
NM_025184.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.587
Genes affected
EFHC2 (HGNC:26233): (EF-hand domain containing 2) This gene encodes a protein which contains three DM10 domains and three calcium-binding EF-hand motifs. A related protein is encoded by a gene on chromosome 6. It has been suggested that both proteins are involved in the development of epilepsy (PMID: 15258581, 16112844) and that this gene may be associated with fear recognition in individuals with Turner syndrome. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant X-44248815-G-A is Benign according to our data. Variant chrX-44248815-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2660365.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.587 with no splicing effect.
BS2
?
High Hemizygotes in GnomAd at 4 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFHC2 | NM_025184.4 | c.960C>T | p.Phe320= | synonymous_variant | 6/15 | ENST00000420999.2 | |
EFHC2 | XM_047442535.1 | c.960C>T | p.Phe320= | synonymous_variant | 6/14 | ||
EFHC2 | XM_047442536.1 | c.960C>T | p.Phe320= | synonymous_variant | 6/15 | ||
EFHC2 | XM_006724562.3 | c.372C>T | p.Phe124= | synonymous_variant | 5/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFHC2 | ENST00000420999.2 | c.960C>T | p.Phe320= | synonymous_variant | 6/15 | 1 | NM_025184.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000539 AC: 6AN: 111287Hom.: 0 Cov.: 23 AF XY: 0.000119 AC XY: 4AN XY: 33481
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GnomAD3 exomes AF: 0.0000449 AC: 8AN: 178009Hom.: 0 AF XY: 0.0000623 AC XY: 4AN XY: 64185
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GnomAD4 exome AF: 0.0000768 AC: 84AN: 1093190Hom.: 0 Cov.: 28 AF XY: 0.0000947 AC XY: 34AN XY: 358870
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GnomAD4 genome ? AF: 0.0000539 AC: 6AN: 111287Hom.: 0 Cov.: 23 AF XY: 0.000119 AC XY: 4AN XY: 33481
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | EFHC2: BP4, BP7, BS2 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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