7-143478061-G-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_176883.2(TAS2R41):​c.189G>T​(p.Thr63Thr) 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: 31)

Consequence

TAS2R41
NM_176883.2 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.143
Variant links:
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]
EPHA1-AS1 (HGNC:27799): (EPHA1 antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP7
Synonymous conserved (PhyloP=0.143 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TAS2R41NM_176883.2 linkc.189G>T p.Thr63Thr synonymous_variant Exon 1 of 1 ENST00000408916.1 NP_795364.2 P59536
EPHA1-AS1NR_033897.1 linkn.207-26713G>T intron_variant Intron 2 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TAS2R41ENST00000408916.1 linkc.189G>T p.Thr63Thr synonymous_variant Exon 1 of 1 6 NM_176883.2 ENSP00000386201.1 P59536
EPHA1-AS1ENST00000429289.5 linkn.207-26713G>T intron_variant Intron 2 of 4 1
EPHA1-AS1ENST00000690912.1 linkn.228-17905G>T intron_variant Intron 2 of 2
EPHA1-AS1ENST00000703017.1 linkn.206-17905G>T intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
48
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
1.5
DANN
Benign
0.60

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-143175154; API