14-102376439-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_014844.5(TECPR2):c.-72-211A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0272 in 152,272 control chromosomes in the GnomAD database, including 74 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 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TECPR2 | NM_014844.5 | c.-72-211A>G | intron_variant | Intron 1 of 19 | ENST00000359520.12 | NP_055659.2 | ||
TECPR2 | NM_001172631.3 | c.-72-211A>G | intron_variant | Intron 1 of 16 | NP_001166102.1 | |||
LOC124903389 | XR_007064350.1 | n.73-5954T>C | intron_variant | Intron 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TECPR2 | ENST00000359520.12 | c.-72-211A>G | intron_variant | Intron 1 of 19 | 1 | NM_014844.5 | ENSP00000352510.7 | |||
TECPR2 | ENST00000558678.1 | c.-72-211A>G | intron_variant | Intron 1 of 16 | 1 | ENSP00000453671.1 | ||||
TECPR2 | ENST00000561228.1 | n.57-211A>G | intron_variant | Intron 1 of 5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0272 AC: 4144AN: 152154Hom.: 74 Cov.: 32
GnomAD4 genome AF: 0.0272 AC: 4144AN: 152272Hom.: 74 Cov.: 32 AF XY: 0.0276 AC XY: 2055AN XY: 74458
ClinVar
Submissions by phenotype
not provided 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