2-1414416-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001206744.2(TPO):c.8C>T(p.Ala3Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000186 in 1,613,498 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A3A) has been classified as Likely benign.
Frequency
Consequence
NM_001206744.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TPO | NM_001206744.2 | c.8C>T | p.Ala3Val | missense_variant | 2/17 | ENST00000329066.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TPO | ENST00000329066.9 | c.8C>T | p.Ala3Val | missense_variant | 2/17 | 1 | NM_001206744.2 | P1 | |
ENST00000650512.1 | n.646+3947G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00103 AC: 156AN: 152076Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000311 AC: 78AN: 250534Hom.: 0 AF XY: 0.000332 AC XY: 45AN XY: 135418
GnomAD4 exome AF: 0.0000985 AC: 144AN: 1461304Hom.: 0 Cov.: 29 AF XY: 0.0000977 AC XY: 71AN XY: 726888
GnomAD4 genome AF: 0.00103 AC: 156AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.000927 AC XY: 69AN XY: 74402
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at