chr6-35136198-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001370687.1(TCP11):c.145A>T(p.Thr49Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,461,366 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
Frequency
Consequence
NM_001370687.1 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 |
---|---|---|---|---|---|---|---|
TCP11 | NM_001370687.1 | c.145A>T | p.Thr49Ser | missense_variant | 3/10 | ENST00000311875.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TCP11 | ENST00000311875.11 | c.145A>T | p.Thr49Ser | missense_variant | 3/10 | 1 | NM_001370687.1 | P3 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248678Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134934
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461366Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 726944
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | The c.184A>T (p.T62S) alteration is located in exon 3 (coding exon 3) of the TCP11 gene. This alteration results from a A to T substitution at nucleotide position 184, causing the threonine (T) at amino acid position 62 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