2-43231255-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022065.5(THADA):c.5555T>C(p.Phe1852Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000203 in 1,612,580 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (★).
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.5555T>C | p.Phe1852Ser | missense_variant | 38/38 | ENST00000405975.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THADA | ENST00000405975.7 | c.5555T>C | p.Phe1852Ser | missense_variant | 38/38 | 1 | NM_022065.5 | P1 | |
ENST00000423354.1 | n.45-1509A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000727 AC: 18AN: 247506Hom.: 0 AF XY: 0.0000893 AC XY: 12AN XY: 134362
GnomAD4 exome AF: 0.000212 AC: 309AN: 1460420Hom.: 1 Cov.: 31 AF XY: 0.000205 AC XY: 149AN XY: 726490
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 08, 2023 | The c.5555T>C (p.F1852S) alteration is located in exon 38 (coding exon 37) of the THADA gene. This alteration results from a T to C substitution at nucleotide position 5555, causing the phenylalanine (F) at amino acid position 1852 to be replaced by a serine (S). 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