4-48228500-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003215.3(TEC):āc.115A>Gā(p.Thr39Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000732 in 1,611,154 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_003215.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TEC | NM_003215.3 | c.115A>G | p.Thr39Ala | missense_variant | 2/18 | ENST00000381501.8 | NP_003206.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TEC | ENST00000381501.8 | c.115A>G | p.Thr39Ala | missense_variant | 2/18 | 1 | NM_003215.3 | ENSP00000370912 | P1 | |
TEC | ENST00000505452.5 | c.115A>G | p.Thr39Ala | missense_variant, NMD_transcript_variant | 1/16 | 5 | ENSP00000424567 |
Frequencies
GnomAD3 genomes AF: 0.000414 AC: 63AN: 152184Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000922 AC: 23AN: 249500Hom.: 0 AF XY: 0.0000890 AC XY: 12AN XY: 134906
GnomAD4 exome AF: 0.0000377 AC: 55AN: 1458852Hom.: 0 Cov.: 30 AF XY: 0.0000455 AC XY: 33AN XY: 725744
GnomAD4 genome AF: 0.000414 AC: 63AN: 152302Hom.: 1 Cov.: 32 AF XY: 0.000403 AC XY: 30AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 19, 2024 | The c.115A>G (p.T39A) alteration is located in exon 2 (coding exon 1) of the TEC gene. This alteration results from a A to G substitution at nucleotide position 115, causing the threonine (T) at amino acid position 39 to be replaced by an alanine (A). 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