14-102376702-A-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_014844.5(TECPR2):c.-20A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.034 in 1,608,772 control chromosomes in the GnomAD database, including 1,080 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_014844.5 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TECPR2 | NM_014844.5 | c.-20A>C | 5_prime_UTR_variant | Exon 2 of 20 | ENST00000359520.12 | NP_055659.2 | ||
TECPR2 | NM_001172631.3 | c.-20A>C | 5_prime_UTR_variant | Exon 2 of 17 | NP_001166102.1 | |||
LOC124903389 | XR_007064350.1 | n.73-6217T>G | intron_variant | Intron 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TECPR2 | ENST00000359520 | c.-20A>C | 5_prime_UTR_variant | Exon 2 of 20 | 1 | NM_014844.5 | ENSP00000352510.7 | |||
TECPR2 | ENST00000558678 | c.-20A>C | 5_prime_UTR_variant | Exon 2 of 17 | 1 | ENSP00000453671.1 | ||||
TECPR2 | ENST00000561228.1 | n.109A>C | non_coding_transcript_exon_variant | Exon 2 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0399 AC: 6068AN: 152142Hom.: 138 Cov.: 32
GnomAD3 exomes AF: 0.0385 AC: 9665AN: 251054Hom.: 241 AF XY: 0.0375 AC XY: 5082AN XY: 135688
GnomAD4 exome AF: 0.0334 AC: 48676AN: 1456512Hom.: 942 Cov.: 30 AF XY: 0.0332 AC XY: 24094AN XY: 724950
GnomAD4 genome AF: 0.0398 AC: 6067AN: 152260Hom.: 138 Cov.: 32 AF XY: 0.0398 AC XY: 2960AN XY: 74438
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. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at