rs1404635
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_176883.2(TAS2R41):c.189G>A(p.Thr63=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 1,613,844 control chromosomes in the GnomAD database, including 60,774 homozygotes. 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: 𝑓 0.22 ( 4429 hom., cov: 31)
Exomes 𝑓: 0.27 ( 56345 hom. )
Consequence
TAS2R41
NM_176883.2 synonymous
NM_176883.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.143
Genes affected
TAS2R41 (HGNC:18883): (taste 2 receptor member 41) This gene encodes a member of the bitter taste receptor family which belong to the G protein-coupled receptor superfamily and are predominantly expressed in taste receptor cells of the tongue and palate epithelia. This intronless taste receptor gene encodes a seven-transmembrane receptor protein, functioning as a bitter taste receptor. This gene is clustered together with eight other taste receptor genes on chromosome 7. Chloramphenicol is an agonist for the encoded protein. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP7
?
Synonymous conserved (PhyloP=0.143 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAS2R41 | NM_176883.2 | c.189G>A | p.Thr63= | synonymous_variant | 1/1 | ENST00000408916.1 | |
EPHA1-AS1 | NR_033897.1 | n.207-26713G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAS2R41 | ENST00000408916.1 | c.189G>A | p.Thr63= | synonymous_variant | 1/1 | NM_176883.2 | P1 | ||
EPHA1-AS1 | ENST00000429289.5 | n.207-26713G>A | intron_variant, non_coding_transcript_variant | 1 | |||||
EPHA1-AS1 | ENST00000690912.1 | n.228-17905G>A | intron_variant, non_coding_transcript_variant | ||||||
EPHA1-AS1 | ENST00000703017.1 | n.206-17905G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.219 AC: 33214AN: 151846Hom.: 4420 Cov.: 31
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GnomAD3 exomes AF: 0.266 AC: 66240AN: 249162Hom.: 9242 AF XY: 0.270 AC XY: 36547AN XY: 135182
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GnomAD4 exome AF: 0.275 AC: 401645AN: 1461880Hom.: 56345 Cov.: 48 AF XY: 0.277 AC XY: 201104AN XY: 727240
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GnomAD4 genome ? AF: 0.219 AC: 33232AN: 151964Hom.: 4429 Cov.: 31 AF XY: 0.223 AC XY: 16531AN XY: 74260
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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