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GeneBe

6-132589267-C-G

Variant summary

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

The NM_003967.3(TAAR5):c.420G>C(p.Leu140=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00119 in 1,609,778 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0064 ( 11 hom., cov: 31)
Exomes 𝑓: 0.00065 ( 5 hom. )

Consequence

TAAR5
NM_003967.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.223
Variant links:
Genes affected
TAAR5 (HGNC:30236): (trace amine associated receptor 5) Enables trimethylamine receptor activity. Predicted to be involved in signal transduction. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

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=-0.7).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 6-132589267-C-G is Benign according to our data. Variant chr6-132589267-C-G is described in ClinVar as [Benign]. Clinvar id is 710993.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=0.223 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 = 0.0064 (974/152154) while in subpopulation AFR AF= 0.0215 (891/41502). AF 95% confidence interval is 0.0203. There are 11 homozygotes in gnomad4. There are 459 alleles in male gnomad4 subpopulation. Median coverage is 31. 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 11 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TAAR5NM_003967.3 linkuse as main transcriptc.420G>C p.Leu140= synonymous_variant 1/1 ENST00000258034.4
TAAR5NM_001389527.1 linkuse as main transcriptc.420G>C p.Leu140= synonymous_variant 4/4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TAAR5ENST00000258034.4 linkuse as main transcriptc.420G>C p.Leu140= synonymous_variant 1/1 NM_003967.3 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00641
AC:
975
AN:
152036
Hom.:
11
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0216
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00399
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0000882
Gnomad OTH
AF:
0.00670
GnomAD3 exomes
AF:
0.00170
AC:
419
AN:
246388
Hom.:
7
AF XY:
0.00128
AC XY:
170
AN XY:
132778
show subpopulations
Gnomad AFR exome
AF:
0.0221
Gnomad AMR exome
AF:
0.00128
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000471
Gnomad NFE exome
AF:
0.0000989
Gnomad OTH exome
AF:
0.000668
GnomAD4 exome
AF:
0.000650
AC:
947
AN:
1457624
Hom.:
5
Cov.:
30
AF XY:
0.000589
AC XY:
427
AN XY:
724682
show subpopulations
Gnomad4 AFR exome
AF:
0.0214
Gnomad4 AMR exome
AF:
0.00146
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000235
Gnomad4 FIN exome
AF:
0.0000376
Gnomad4 NFE exome
AF:
0.0000595
Gnomad4 OTH exome
AF:
0.00153
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00640
AC:
974
AN:
152154
Hom.:
11
Cov.:
31
AF XY:
0.00617
AC XY:
459
AN XY:
74398
show subpopulations
Gnomad4 AFR
AF:
0.0215
Gnomad4 AMR
AF:
0.00399
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000882
Gnomad4 OTH
AF:
0.00664
Alfa
AF:
0.00192
Hom.:
1
Bravo
AF:
0.00774
Asia WGS
AF:
0.000289
AC:
1
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 testingInvitaeAug 20, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.70
Cadd
Benign
5.3
Dann
Benign
0.71

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs142165413; hg19: chr6-132910406; API