Variant 19-9251667-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001079935.2(OR7E24):c.624C>T(p.Ser208=) 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

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 made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR7E24	NM_001079935.2 linkuse as main transcript	c.624C>T	p.Ser208=	synonymous_variant	1/1	ENST00000456448.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR7E24	ENST00000456448.3 linkuse as main transcript	c.624C>T	p.Ser208=	synonymous_variant	1/1		NM_001079935.2	P2
OR7E24	ENST00000641946.1 linkuse as main transcript	c.612C>T	p.Ser204=	synonymous_variant	2/2			A2

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

GnomAD3 exomes

AF:

0.372

AC:

92513

AN:

248806

Hom.:

19873

AF XY:

0.362

AC XY:

48863

AN XY:

135014

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 SAS exome

AF:

0.412

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

Gnomad4 AFR exome

AF:

0.780

Gnomad4 AMR exome

AF:

0.431

Gnomad4 ASJ exome

AF:

0.236

Gnomad4 EAS exome

AF:

0.550

Gnomad4 SAS exome

AF:

0.409

Gnomad4 FIN exome

AF:

0.392

Gnomad4 NFE exome

AF:

0.258

Gnomad4 OTH exome

AF:

0.326

GnomAD4 genome

AF:

0.433

AC:

65871

AN:

152018

Hom.:

17775

Cov.:

AF XY:

0.441

AC XY:

32772

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.757

Gnomad4 AMR

AF:

0.383

Gnomad4 ASJ

AF:

0.234

Gnomad4 EAS

AF:

0.548

Gnomad4 SAS

AF:

0.417

Gnomad4 FIN

AF:

0.392

Gnomad4 NFE

AF:

0.262

Gnomad4 OTH

AF:

0.378

Alfa

AF:

0.294

Hom.:

12245

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

Cadd

Benign

7.9

Dann

Benign

0.40

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over