1-15427219-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_024329.6(EFHD2):c.526C>T(p.Arg176Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000435 in 1,608,522 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R176H) has been classified as Uncertain significance.
Frequency
Consequence
NM_024329.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFHD2 | NM_024329.6 | c.526C>T | p.Arg176Cys | missense_variant | 3/4 | ENST00000375980.9 | |
EFHD2 | XM_005246000.4 | c.456+1201C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFHD2 | ENST00000375980.9 | c.526C>T | p.Arg176Cys | missense_variant | 3/4 | 1 | NM_024329.6 | P1 | |
EFHD2 | ENST00000445566.1 | c.235C>T | p.Arg79Cys | missense_variant | 3/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000126 AC: 3AN: 237834Hom.: 0 AF XY: 0.00000775 AC XY: 1AN XY: 128964
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1456316Hom.: 0 Cov.: 32 AF XY: 0.00000414 AC XY: 3AN XY: 723864
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | The c.526C>T (p.R176C) alteration is located in exon 3 (coding exon 3) of the EFHD2 gene. This alteration results from a C to T substitution at nucleotide position 526, causing the arginine (R) at amino acid position 176 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at