chr2-43230958-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022065.5(THADA):c.5852C>T(p.Ala1951Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000128 in 1,604,154 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign 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. A1951G) has been classified as Likely benign.
Frequency
Consequence
NM_022065.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THADA | NM_022065.5 | c.5852C>T | p.Ala1951Val | missense_variant | 38/38 | ENST00000405975.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THADA | ENST00000405975.7 | c.5852C>T | p.Ala1951Val | missense_variant | 38/38 | 1 | NM_022065.5 | P1 | |
ENST00000423354.1 | n.44+1342G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000849 AC: 21AN: 247348Hom.: 0 AF XY: 0.0000820 AC XY: 11AN XY: 134208
GnomAD4 exome AF: 0.000136 AC: 197AN: 1452074Hom.: 0 Cov.: 31 AF XY: 0.000124 AC XY: 89AN XY: 720392
GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2022 | The c.5852C>T (p.A1951V) alteration is located in exon 38 (coding exon 37) of the THADA gene. This alteration results from a C to T substitution at nucleotide position 5852, causing the alanine (A) at amino acid position 1951 to be replaced by a valine (V). 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