2-43231335-T-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_022065.5(THADA):āc.5475A>Cā(p.Glu1825Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000505 in 1,541,950 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_022065.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
THADA | NM_022065.5 | c.5475A>C | p.Glu1825Asp | missense_variant | 38/38 | ENST00000405975.7 | NP_071348.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
THADA | ENST00000405975.7 | c.5475A>C | p.Glu1825Asp | missense_variant | 38/38 | 1 | NM_022065.5 | ENSP00000386088.2 |
Frequencies
GnomAD3 genomes AF: 0.00252 AC: 384AN: 152188Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000861 AC: 146AN: 169644Hom.: 0 AF XY: 0.000667 AC XY: 60AN XY: 89888
GnomAD4 exome AF: 0.000284 AC: 394AN: 1389644Hom.: 1 Cov.: 30 AF XY: 0.000251 AC XY: 172AN XY: 684994
GnomAD4 genome AF: 0.00252 AC: 384AN: 152306Hom.: 1 Cov.: 32 AF XY: 0.00239 AC XY: 178AN XY: 74488
ClinVar
Submissions by phenotype
THADA-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 24, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at