X-44148885-A-G
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_025184.4(EFHC2):āc.2160T>Cā(p.Asp720Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000145 in 1,174,682 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 62 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00020 ( 0 hom., 8 hem., cov: 23)
Exomes š: 0.00014 ( 0 hom. 54 hem. )
Consequence
EFHC2
NM_025184.4 synonymous
NM_025184.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.95
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=-0.73).
BP6
Variant X-44148885-A-G is Benign according to our data. Variant chrX-44148885-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2660362.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.95 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 8 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EFHC2 | NM_025184.4 | c.2160T>C | p.Asp720Asp | synonymous_variant | 15/15 | ENST00000420999.2 | NP_079460.2 | |
EFHC2 | XM_047442535.1 | c.2067T>C | p.Asp689Asp | synonymous_variant | 14/14 | XP_047298491.1 | ||
EFHC2 | XM_006724562.3 | c.1572T>C | p.Asp524Asp | synonymous_variant | 14/14 | XP_006724625.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000205 AC: 23AN: 112213Hom.: 0 Cov.: 23 AF XY: 0.000233 AC XY: 8AN XY: 34359
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GnomAD3 exomes AF: 0.000346 AC: 44AN: 127114Hom.: 0 AF XY: 0.000416 AC XY: 16AN XY: 38430
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GnomAD4 exome AF: 0.000138 AC: 147AN: 1062469Hom.: 0 Cov.: 28 AF XY: 0.000157 AC XY: 54AN XY: 343585
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GnomAD4 genome AF: 0.000205 AC: 23AN: 112213Hom.: 0 Cov.: 23 AF XY: 0.000233 AC XY: 8AN XY: 34359
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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 | Feb 01, 2023 | EFHC2: BP4, BP7, BS2 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at