chr1-18844452-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152232.6(TAS1R2):c.1468-2600T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,106 control chromosomes in the GnomAD database, including 33,885 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 0.66 ( 33885 hom., cov: 32)
Consequence
TAS1R2
NM_152232.6 intron
NM_152232.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.00100
Publications
0 publications found
Genes affected
TAS1R2 (HGNC:14905): (taste 1 receptor member 2) Contributes to sweet taste receptor activity. Involved in detection of chemical stimulus involved in sensory perception of sweet taste and positive regulation of cytokinesis. Part of sweet taste receptor complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.662 AC: 100678AN: 151986Hom.: 33874 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
100678
AN:
151986
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.662 AC: 100717AN: 152106Hom.: 33885 Cov.: 32 AF XY: 0.657 AC XY: 48859AN XY: 74334 show subpopulations
GnomAD4 genome
AF:
AC:
100717
AN:
152106
Hom.:
Cov.:
32
AF XY:
AC XY:
48859
AN XY:
74334
show subpopulations
African (AFR)
AF:
AC:
23465
AN:
41470
American (AMR)
AF:
AC:
10051
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
2284
AN:
3470
East Asian (EAS)
AF:
AC:
2865
AN:
5176
South Asian (SAS)
AF:
AC:
2692
AN:
4822
European-Finnish (FIN)
AF:
AC:
7303
AN:
10566
Middle Eastern (MID)
AF:
AC:
186
AN:
294
European-Non Finnish (NFE)
AF:
AC:
49790
AN:
67994
Other (OTH)
AF:
AC:
1391
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1700
3400
5100
6800
8500
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
802
1604
2406
3208
4010
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1872
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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