rs201224382
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_015395.3(TECPR1):c.3396C>T(p.Asp1132Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Consequence
TECPR1
NM_015395.3 synonymous
NM_015395.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.847
Genes affected
TECPR1 (HGNC:22214): (tectonin beta-propeller repeat containing 1) This gene encodes a tethering factor involved in autophagy. The encoded protein is found at autolysosomes, and is involved in targeting protein aggregates, damaged mitochondria, and bacterial pathogens for autophagy [provided by RefSeq, Nov 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP7
Synonymous conserved (PhyloP=-0.847 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TECPR1 | NM_015395.3 | c.3396C>T | p.Asp1132Asp | synonymous_variant | Exon 26 of 26 | ENST00000447648.7 | NP_056210.1 | |
TECPR1 | XM_005250253.5 | c.3396C>T | p.Asp1132Asp | synonymous_variant | Exon 26 of 26 | XP_005250310.1 | ||
TECPR1 | XM_017011937.2 | c.3294C>T | p.Asp1098Asp | synonymous_variant | Exon 25 of 25 | XP_016867426.1 | ||
TECPR1 | XM_047420119.1 | c.3294C>T | p.Asp1098Asp | synonymous_variant | Exon 25 of 25 | XP_047276075.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TECPR1 | ENST00000447648.7 | c.3396C>T | p.Asp1132Asp | synonymous_variant | Exon 26 of 26 | 1 | NM_015395.3 | ENSP00000404923.2 | ||
TECPR1 | ENST00000490842.5 | n.2594C>T | non_coding_transcript_exon_variant | Exon 15 of 16 | 1 | |||||
TECPR1 | ENST00000463402.5 | n.908C>T | non_coding_transcript_exon_variant | Exon 5 of 5 | 2 | |||||
TECPR1 | ENST00000485716.1 | n.159C>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at