dbSNP rs4144146: TAAR5:c.-47-5521C>T (chr6-132595254-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001389527.1(TAAR5):c.-47-5521C>T variant causes a intron change. The variant allele was found at a frequency of 0.144 in 153,460 control chromosomes in the GnomAD database, including 2,142 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 0.14 ( 2138 hom., cov: 31)

Exomes 𝑓: 0.043 ( 4 hom. )

Consequence

TAAR5
NM_001389527.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.28

Publications

2 publications found

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]

TAAR5 links:

TAAR4P (HGNC:31924): (trace amine associated receptor 4, pseudogene) Predicted to enable 2-phenylethylamine receptor activity. Predicted to be involved in behavioral fear response; chemosensory behavior; and sensory perception of chemical stimulus. [provided by Alliance of Genome Resources, Apr 2022]

TAAR4P links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.3).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001389527.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAAR5	NM_001389527.1		c.-47-5521C>T		intron	N/A	NP_001376456.1	O14804

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAAR4P	ENST00000454843.1	TSL:6	n.183C>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

22009

AN:

151956

Hom.:

2136

Cov.:

show subpopulations

Gnomad AFR

AF:

0.267

Gnomad AMI

AF:

0.177

Gnomad AMR

AF:

0.109

Gnomad ASJ

AF:

0.113

Gnomad EAS

AF:

0.257

Gnomad SAS

AF:

0.181

Gnomad FIN

AF:

0.0717

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.0804

Gnomad OTH

AF:

0.143

GnomAD4 exome

AF:

0.0433

AC:

AN:

1386

Hom.:

Cov.:

AF XY:

0.0450

AC XY:

AN XY:

800

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.286

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.167

AC:

AN:

South Asian (SAS)

AF:

0.333

AC:

AN:

European-Finnish (FIN)

AF:

0.0245

AC:

AN:

898

Middle Eastern (MID)

AF:

0.0833

AC:

AN:

108

European-Non Finnish (NFE)

AF:

0.0500

AC:

AN:

300

Other (OTH)

AF:

0.146

AC:

AN:

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0000000000000281997), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.386

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.145

AC:

22036

AN:

152074

Hom.:

2138

Cov.:

AF XY:

0.146

AC XY:

10881

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.267

AC:

11051

AN:

41436

American (AMR)

AF:

0.109

AC:

1670

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.113

AC:

392

AN:

3472

East Asian (EAS)

AF:

0.258

AC:

1333

AN:

5166

South Asian (SAS)

AF:

0.181

AC:

870

AN:

4814

European-Finnish (FIN)

AF:

0.0717

AC:

760

AN:

10604

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0803

AC:

5463

AN:

68000

Other (OTH)

AF:

0.144

AC:

304

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

890

1780

2671

3561

4451

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

236

472

708

944

1180

<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:

0.116

Hom.:

636

Bravo

AF:

0.153

Asia WGS

AF:

0.231

AC:

801

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.30

CADD

Benign

(source)

DANN

Benign

0.93

PhyloP100

4.3

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over