rs307374
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152228.3(TAS1R3):c.*515T>A variant causes a 3 prime UTR 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: 36)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TAS1R3
NM_152228.3 3_prime_UTR
NM_152228.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.919
Genes affected
TAS1R3 (HGNC:15661): (taste 1 receptor member 3) The protein encoded by this gene is a G-protein coupled receptor involved in taste responses. The encoded protein can form a heterodimeric receptor with TAS1R1 to elicit the umami taste response, or it can bind with TAS1R2 to form a receptor for the sweet taste response. [provided by RefSeq, Nov 2015]
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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=-0.83).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAS1R3 | NM_152228.3 | c.*515T>A | 3_prime_UTR_variant | 6/6 | ENST00000339381.6 | ||
TAS1R3 | XM_017002435.2 | c.*515T>A | 3_prime_UTR_variant | 5/5 | |||
TAS1R3 | XM_017002436.2 | c.*515T>A | 3_prime_UTR_variant | 5/5 | |||
TAS1R3 | XM_047431571.1 | c.*515T>A | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAS1R3 | ENST00000339381.6 | c.*515T>A | 3_prime_UTR_variant | 6/6 | 2 | NM_152228.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 36
GnomAD3 genomes
?
Cov.:
36
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 2886Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 1464
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
2886
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
1464
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 36
GnomAD4 genome
?
Cov.:
36
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at