chr1-6576401-C-G
Position:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138697.4(TAS1R1):c.1261-14C>G variant causes a splice polypyrimidine tract, intron 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: 32)
Consequence
TAS1R1
NM_138697.4 splice_polypyrimidine_tract, intron
NM_138697.4 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.44
Genes affected
TAS1R1 (HGNC:14448): (taste 1 receptor member 1) The protein encoded by this gene is a G protein-coupled receptor and is a component of the heterodimeric amino acid taste receptor T1R1+3. The T1R1+3 receptor responds to L-amino acids but not to D-enantiomers or other compounds. Most amino acids that are perceived as sweet activate T1R1+3, and this activation is strictly dependent on an intact T1R1+3 heterodimer. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAS1R1 | NM_138697.4 | c.1261-14C>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000333172.11 | |||
LOC107984912 | XR_002958250.1 | n.87+2946G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAS1R1 | ENST00000333172.11 | c.1261-14C>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_138697.4 | P1 | |||
TAS1R1 | ENST00000415267.1 | c.276-14C>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
TAS1R1 | ENST00000351136.7 | c.499-14C>G | splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
TAS1R1 | ENST00000411823.5 | c.1037+1009C>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 38
GnomAD4 exome
Cov.:
38
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
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