2-43232874-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022065.5(THADA):c.5305T>G(p.Phe1769Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,609,316 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022065.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THADA | NM_022065.5 | c.5305T>G | p.Phe1769Val | missense_variant | 37/38 | ENST00000405975.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THADA | ENST00000405975.7 | c.5305T>G | p.Phe1769Val | missense_variant | 37/38 | 1 | NM_022065.5 | P1 | |
ENST00000423354.1 | n.155A>C | non_coding_transcript_exon_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000208 AC: 5AN: 240104Hom.: 0 AF XY: 0.0000154 AC XY: 2AN XY: 130156
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1457082Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 724198
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.5305T>G (p.F1769V) alteration is located in exon 37 (coding exon 36) of the THADA gene. This alteration results from a T to G substitution at nucleotide position 5305, causing the phenylalanine (F) at amino acid position 1769 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