Genetic Variant NM_001317107.2:c.*106C>T (chr14-21669882-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001317107.2(OR4E1):c.*106C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 396,224 control chromosomes in the GnomAD database, including 7,616 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 0.19 ( 3181 hom., cov: 32)

Exomes 𝑓: 0.18 ( 4435 hom. )

Consequence

OR4E1
NM_001317107.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.706

Publications

2 publications found

Variant links:

Genes affected

OR4E1 (HGNC:8296): (olfactory receptor family 4 subfamily E member 1) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]

OR4E1 links:

TRA (HGNC:12027):

TRA links:

Genome browser will be placed here

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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR4E1	NM_001317107.2 link	c.*106C>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000641792.2	NP_001304036.1
TRA		n.21669882G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR4E1	ENST00000641792.2 link	c.*106C>T		3_prime_UTR_variant	Exon 2 of 2		NM_001317107.2	ENSP00000493111.1

Frequencies

GnomAD3 genomes

AF:

0.195

AC:

29590

AN:

151968

Hom.:

3185

Cov.:

show subpopulations

Gnomad AFR

AF:

0.248

Gnomad AMI

AF:

0.0384

Gnomad AMR

AF:

0.169

Gnomad ASJ

AF:

0.257

Gnomad EAS

AF:

0.00750

Gnomad SAS

AF:

0.0569

Gnomad FIN

AF:

0.122

Gnomad MID

AF:

0.185

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.205

GnomAD4 exome

AF:

0.179

AC:

43623

AN:

244134

Hom.:

4435

Cov.:

AF XY:

0.180

AC XY:

22340

AN XY:

123788

show subpopulations

African (AFR)

AF:

0.247

AC:

1764

AN:

7134

American (AMR)

AF:

0.151

AC:

1112

AN:

7378

Ashkenazi Jewish (ASJ)

AF:

0.261

AC:

2405

AN:

9200

East Asian (EAS)

AF:

0.00981

AC:

224

AN:

22824

South Asian (SAS)

AF:

0.0586

AC:

128

AN:

2186

European-Finnish (FIN)

AF:

0.125

AC:

2595

AN:

20688

Middle Eastern (MID)

AF:

0.187

AC:

240

AN:

1282

European-Non Finnish (NFE)

AF:

0.204

AC:

32010

AN:

157166

Other (OTH)

AF:

0.193

AC:

3145

AN:

16276

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1727

3455

5182

6910

8637

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

146

292

438

584

730

<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:

0.195

AC:

29593

AN:

152090

Hom.:

3181

Cov.:

AF XY:

0.187

AC XY:

13899

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.248

AC:

10277

AN:

41446

American (AMR)

AF:

0.169

AC:

2580

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.257

AC:

890

AN:

3468

East Asian (EAS)

AF:

0.00752

AC:

AN:

5186

South Asian (SAS)

AF:

0.0559

AC:

269

AN:

4810

European-Finnish (FIN)

AF:

0.122

AC:

1293

AN:

10586

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.202

AC:

13725

AN:

67988

Other (OTH)

AF:

0.203

AC:

430

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1208

2416

3625

4833

6041

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

304

608

912

1216

1520

<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:

0.194

Hom.:

1612

Bravo

AF:

0.203

Asia WGS

AF:

0.0440

AC:

153

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.6

(source)

DANN

Benign

0.63

PhyloP100

-0.71

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