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GeneBe

1-6570918-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_138697.4(TAS1R1):c.201C>T(p.Ser67=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00162 in 1,599,856 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0083 ( 15 hom., cov: 32)
Exomes 𝑓: 0.00091 ( 24 hom. )

Consequence

TAS1R1
NM_138697.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0140
Variant links:
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 Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-6570918-C-T is Benign according to our data. Variant chr1-6570918-C-T is described in ClinVar as [Benign]. Clinvar id is 775496.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.014 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00834 (1270/152312) while in subpopulation AFR AF= 0.0287 (1193/41570). AF 95% confidence interval is 0.0273. There are 15 homozygotes in gnomad4. There are 579 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 16 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TAS1R1NM_138697.4 linkuse as main transcriptc.201C>T p.Ser67= synonymous_variant 2/6 ENST00000333172.11
LOC107984912XR_002958250.1 linkuse as main transcriptn.88-935G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TAS1R1ENST00000333172.11 linkuse as main transcriptc.201C>T p.Ser67= synonymous_variant 2/61 NM_138697.4 P1Q7RTX1-1
TAS1R1ENST00000351136.7 linkuse as main transcriptc.201C>T p.Ser67= synonymous_variant 2/52 Q7RTX1-2
TAS1R1ENST00000415267.1 linkuse as main transcript upstream_gene_variant 1
TAS1R1ENST00000411823.5 linkuse as main transcript upstream_gene_variant 2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00833
AC:
1268
AN:
152194
Hom.:
16
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0287
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00321
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000118
Gnomad OTH
AF:
0.00958
GnomAD3 exomes
AF:
0.00263
AC:
623
AN:
236578
Hom.:
14
AF XY:
0.00202
AC XY:
256
AN XY:
126970
show subpopulations
Gnomad AFR exome
AF:
0.0336
Gnomad AMR exome
AF:
0.00163
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000160
Gnomad OTH exome
AF:
0.00121
GnomAD4 exome
AF:
0.000909
AC:
1316
AN:
1447544
Hom.:
24
Cov.:
31
AF XY:
0.000757
AC XY:
544
AN XY:
718770
show subpopulations
Gnomad4 AFR exome
AF:
0.0310
Gnomad4 AMR exome
AF:
0.00189
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000362
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000606
Gnomad4 OTH exome
AF:
0.00205
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00834
AC:
1270
AN:
152312
Hom.:
15
Cov.:
32
AF XY:
0.00777
AC XY:
579
AN XY:
74472
show subpopulations
Gnomad4 AFR
AF:
0.0287
Gnomad4 AMR
AF:
0.00320
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000118
Gnomad4 OTH
AF:
0.00948
Alfa
AF:
0.00532
Hom.:
4
Bravo
AF:
0.0102
Asia WGS
AF:
0.00260
AC:
9
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeMay 31, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
Cadd
Benign
6.8
Dann
Benign
0.51

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs61746701; hg19: chr1-6630978; API