chr16-75647931-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018975.4(TERF2IP):c.49T>C(p.Ser17Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S17S) has been classified as Likely benign.
Frequency
Consequence
NM_018975.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TERF2IP | NM_018975.4 | c.49T>C | p.Ser17Pro | missense_variant | 1/3 | ENST00000300086.5 | |
TERF2IP | XM_047434216.1 | c.49T>C | p.Ser17Pro | missense_variant | 1/2 | ||
TERF2IP | NR_144545.2 | n.159T>C | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TERF2IP | ENST00000300086.5 | c.49T>C | p.Ser17Pro | missense_variant | 1/3 | 1 | NM_018975.4 | P1 | |
KARS1 | ENST00000566560.5 | n.176+537A>G | intron_variant, non_coding_transcript_variant | 1 | |||||
TERF2IP | ENST00000653858.1 | c.49T>C | p.Ser17Pro | missense_variant | 1/4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 11, 2023 | The p.S17P variant (also known as c.49T>C), located in coding exon 1 of the TERF2IP gene, results from a T to C substitution at nucleotide position 49. The serine at codon 17 is replaced by proline, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.