Variant chr11-48307092-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_001004725.1(OR4S1):c.870C>T(p.Asn290=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 1,612,636 control chromosomes in the GnomAD database, including 85,863 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 0.36 ( 10501 hom., cov: 31)

Exomes 𝑓: 0.31 ( 75362 hom. )

Consequence

OR4S1
NM_001004725.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.35

Variant links:

Genes affected

OR4S1 (HGNC:14705): (olfactory receptor family 4 subfamily S 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]

OR4S1 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=-0.87).

BP7

Synonymous conserved (PhyloP=-1.35 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR4S1	NM_001004725.1 linkuse as main transcript	c.870C>T	p.Asn290=	synonymous_variant	1/1	ENST00000319988.1	NP_001004725.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR4S1	ENST00000319988.1 linkuse as main transcript	c.870C>T	p.Asn290=	synonymous_variant	1/1		NM_001004725.1	ENSP00000321447	P1

Frequencies

GnomAD3 genomes

AF:

0.357

AC:

54153

AN:

151818

Hom.:

10482

Cov.:

show subpopulations

Gnomad AFR

AF:

0.496

Gnomad AMI

AF:

0.165

Gnomad AMR

AF:

0.297

Gnomad ASJ

AF:

0.346

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.493

Gnomad FIN

AF:

0.218

Gnomad MID

AF:

0.357

Gnomad NFE

AF:

0.294

Gnomad OTH

AF:

0.373

GnomAD3 exomes

AF:

0.329

AC:

82738

AN:

251244

Hom.:

15054

AF XY:

0.339

AC XY:

46016

AN XY:

135756

show subpopulations

Gnomad AFR exome

AF:

0.502

Gnomad AMR exome

AF:

0.217

Gnomad ASJ exome

AF:

0.341

Gnomad EAS exome

AF:

0.419

Gnomad SAS exome

AF:

0.502

Gnomad FIN exome

AF:

0.230

Gnomad NFE exome

AF:

0.295

Gnomad OTH exome

AF:

0.331

GnomAD4 exome

AF:

0.313

AC:

457023

AN:

1460700

Hom.:

75362

Cov.:

AF XY:

0.318

AC XY:

231263

AN XY:

726678

show subpopulations

Gnomad4 AFR exome

AF:

0.511

Gnomad4 AMR exome

AF:

0.226

Gnomad4 ASJ exome

AF:

0.345

Gnomad4 EAS exome

AF:

0.372

Gnomad4 SAS exome

AF:

0.493

Gnomad4 FIN exome

AF:

0.236

Gnomad4 NFE exome

AF:

0.295

Gnomad4 OTH exome

AF:

0.348

GnomAD4 genome

AF:

0.357

AC:

54221

AN:

151936

Hom.:

10501

Cov.:

AF XY:

0.356

AC XY:

26444

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.497

Gnomad4 AMR

AF:

0.298

Gnomad4 ASJ

AF:

0.346

Gnomad4 EAS

AF:

0.424

Gnomad4 SAS

AF:

0.493

Gnomad4 FIN

AF:

0.218

Gnomad4 NFE

AF:

0.294

Gnomad4 OTH

AF:

0.372

Alfa

AF:

0.323

Hom.:

4652

Bravo

AF:

0.363

Asia WGS

AF:

0.509

AC:

1771

AN:

3478

EpiCase

AF:

0.315

EpiControl

AF:

0.322

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.14

DANN

Benign

0.43

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