Genetic Variant OR7E24:p.Ser208Ser (chr19-9251667-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001079935.2(OR7E24):c.624C>T(p.Ser208Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 1,612,410 control chromosomes in the GnomAD database, including 91,571 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 0.43 ( 17775 hom., cov: 32)

Exomes 𝑓: 0.30 ( 73796 hom. )

Consequence

OR7E24
NM_001079935.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.48

Publications

19 publications found

Variant links:

Genes affected

OR7E24 (HGNC:8396): (olfactory receptor family 7 subfamily E member 24) 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]

OR7E24 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP7

Synonymous conserved (PhyloP=-4.48 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001079935.2. 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
	OR7E24	NM_001079935.2	MANE Select	c.624C>T	p.Ser208Ser	synonymous	Exon 1 of 1	NP_001073404.1	Q6IFN5
	OR7E24	NM_001386108.1		c.612C>T	p.Ser204Ser	synonymous	Exon 2 of 2	NP_001373037.1	A0A2R8Y4Q1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR7E24	ENST00000456448.3	TSL:6 MANE Select	c.624C>T	p.Ser208Ser	synonymous	Exon 1 of 1	ENSP00000387523.1	Q6IFN5
	OR7E24	ENST00000641946.1		c.612C>T	p.Ser204Ser	synonymous	Exon 2 of 2	ENSP00000494223.1	A0A2R8Y4Q1

Frequencies

GnomAD3 genomes

AF:

0.433

AC:

65771

AN:

151900

Hom.:

17722

Cov.:

show subpopulations

Gnomad AFR

AF:

0.757

Gnomad AMI

AF:

0.143

Gnomad AMR

AF:

0.383

Gnomad ASJ

AF:

0.234

Gnomad EAS

AF:

0.548

Gnomad SAS

AF:

0.418

Gnomad FIN

AF:

0.392

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.262

Gnomad OTH

AF:

0.381

GnomAD2 exomes

AF:

0.372

AC:

92513

AN:

248806

AF XY:

0.362

show subpopulations

Gnomad AFR exome

AF:

0.766

Gnomad AMR exome

AF:

0.438

Gnomad ASJ exome

AF:

0.231

Gnomad EAS exome

AF:

0.576

Gnomad FIN exome

AF:

0.394

Gnomad NFE exome

AF:

0.265

Gnomad OTH exome

AF:

0.318

GnomAD4 exome

AF:

0.300

AC:

437738

AN:

1460392

Hom.:

73796

Cov.:

AF XY:

0.301

AC XY:

218597

AN XY:

726522

show subpopulations

African (AFR)

AF:

0.780

AC:

26082

AN:

33452

American (AMR)

AF:

0.431

AC:

19241

AN:

44668

Ashkenazi Jewish (ASJ)

AF:

0.236

AC:

6153

AN:

26120

East Asian (EAS)

AF:

0.550

AC:

21838

AN:

39692

South Asian (SAS)

AF:

0.409

AC:

35244

AN:

86212

European-Finnish (FIN)

AF:

0.392

AC:

20904

AN:

53300

Middle Eastern (MID)

AF:

0.316

AC:

1822

AN:

5768

European-Non Finnish (NFE)

AF:

0.258

AC:

286790

AN:

1110866

Other (OTH)

AF:

0.326

AC:

19664

AN:

60314

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

15248

30496

45744

60992

76240

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10014

20028

30042

40056

50070

<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:

0.433

AC:

65871

AN:

152018

Hom.:

17775

Cov.:

AF XY:

0.441

AC XY:

32772

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.757

AC:

31391

AN:

41464

American (AMR)

AF:

0.383

AC:

5845

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.234

AC:

811

AN:

3468

East Asian (EAS)

AF:

0.548

AC:

2835

AN:

5174

South Asian (SAS)

AF:

0.417

AC:

2011

AN:

4824

European-Finnish (FIN)

AF:

0.392

AC:

4142

AN:

10558

Middle Eastern (MID)

AF:

0.340

AC:

100

AN:

294

European-Non Finnish (NFE)

AF:

0.262

AC:

17808

AN:

67960

Other (OTH)

AF:

0.378

AC:

798

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1610

3220

4829

6439

8049

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

562

1124

1686

2248

2810

<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:

0.320

Hom.:

30949

Bravo

AF:

0.447

Asia WGS

AF:

0.484

AC:

1685

AN:

3478

EpiCase

AF:

0.262

EpiControl

AF:

0.260

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

7.9

(source)

DANN

Benign

0.40

PhyloP100

-4.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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