rs199869185
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_080390.4(TCEAL2):c.11T>C(p.Leu4Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,203,473 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 44 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080390.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TCEAL2 | ENST00000372780.6 | c.11T>C | p.Leu4Pro | missense_variant | Exon 3 of 3 | 1 | NM_080390.4 | ENSP00000361866.1 | ||
TCEAL2 | ENST00000476749.1 | n.796T>C | non_coding_transcript_exon_variant | Exon 2 of 2 | 1 | |||||
TCEAL2 | ENST00000329035.2 | c.11T>C | p.Leu4Pro | missense_variant | Exon 3 of 3 | 5 | ENSP00000332359.2 | |||
TCEAL2 | ENST00000651085.1 | n.153+396T>C | intron_variant | Intron 2 of 3 |
Frequencies
GnomAD3 genomes AF: 0.0000267 AC: 3AN: 112159Hom.: 0 Cov.: 24 AF XY: 0.0000582 AC XY: 2AN XY: 34385
GnomAD3 exomes AF: 0.0000342 AC: 6AN: 175405Hom.: 0 AF XY: 0.0000323 AC XY: 2AN XY: 61879
GnomAD4 exome AF: 0.000122 AC: 133AN: 1091314Hom.: 0 Cov.: 31 AF XY: 0.000117 AC XY: 42AN XY: 359340
GnomAD4 genome AF: 0.0000267 AC: 3AN: 112159Hom.: 0 Cov.: 24 AF XY: 0.0000582 AC XY: 2AN XY: 34385
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.11T>C (p.L4P) alteration is located in exon 3 (coding exon 1) of the TCEAL2 gene. This alteration results from a T to C substitution at nucleotide position 11, causing the leucine (L) at amino acid position 4 to be replaced by a proline (P). 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