14-102376694-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_014844.5(TECPR2):c.-28G>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000472 in 1,602,996 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_014844.5 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TECPR2 | ENST00000359520 | c.-28G>A | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 20 | 1 | NM_014844.5 | ENSP00000352510.7 | |||
TECPR2 | ENST00000359520 | c.-28G>A | 5_prime_UTR_variant | Exon 2 of 20 | 1 | NM_014844.5 | ENSP00000352510.7 |
Frequencies
GnomAD3 genomes AF: 0.00222 AC: 338AN: 152130Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.000503 AC: 126AN: 250744Hom.: 1 AF XY: 0.000450 AC XY: 61AN XY: 135516
GnomAD4 exome AF: 0.000290 AC: 421AN: 1450748Hom.: 0 Cov.: 28 AF XY: 0.000275 AC XY: 199AN XY: 722574
GnomAD4 genome AF: 0.00220 AC: 335AN: 152248Hom.: 3 Cov.: 32 AF XY: 0.00212 AC XY: 158AN XY: 74424
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at