12-106321690-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152772.3(TCP11L2):c.619A>T(p.Ile207Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000208 in 1,614,040 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152772.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TCP11L2 | NM_152772.3 | c.619A>T | p.Ile207Phe | missense_variant | Exon 5 of 10 | ENST00000299045.8 | NP_689985.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000994 AC: 25AN: 251422Hom.: 0 AF XY: 0.000132 AC XY: 18AN XY: 135896
GnomAD4 exome AF: 0.000224 AC: 328AN: 1461822Hom.: 0 Cov.: 31 AF XY: 0.000206 AC XY: 150AN XY: 727218
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.619A>T (p.I207F) alteration is located in exon 5 (coding exon 4) of the TCP11L2 gene. This alteration results from a A to T substitution at nucleotide position 619, causing the isoleucine (I) at amino acid position 207 to be replaced by a phenylalanine (F). 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