X-44163957-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_025184.4(EFHC2):c.2113G>A(p.Val705Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000893 in 111,977 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_025184.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EFHC2 | NM_025184.4 | c.2113G>A | p.Val705Met | missense_variant | Exon 14 of 15 | ENST00000420999.2 | NP_079460.2 | |
EFHC2 | XM_047442535.1 | c.2020G>A | p.Val674Met | missense_variant | Exon 13 of 14 | XP_047298491.1 | ||
EFHC2 | XM_006724562.3 | c.1525G>A | p.Val509Met | missense_variant | Exon 13 of 14 | XP_006724625.1 | ||
EFHC2 | XM_047442536.1 | c.*102G>A | 3_prime_UTR_variant | Exon 15 of 15 | XP_047298492.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000893 AC: 1AN: 111977Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34147
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1056398Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 342674
GnomAD4 genome AF: 0.00000893 AC: 1AN: 111977Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34147
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at