Genetic Variant ENST00000454843.1:n.183C>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 ENST00000454843.1(TAAR4P):n.183C>T variant causes a non coding transcript exon 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

TAAR4P
ENST00000454843.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.28

Publications

2 publications found

Variant links:

Genes affected

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:

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:

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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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAAR4P		n.132595254G>A		intragenic_variant
TAAR5	NM_001389527.1 link	c.-47-5521C>T		intron_variant	Intron 3 of 3		NP_001376456.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAAR4P	ENST00000454843.1 link	n.183C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 = 0.000000), 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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over