Variant 11-55554735-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001001920.3(OR4C15):c.267A>G(p.Lys89Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 1,613,484 control chromosomes in the GnomAD database, including 57,883 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 0.24 ( 4924 hom., cov: 32)

Exomes 𝑓: 0.26 ( 52959 hom. )

Consequence

OR4C15
NM_001001920.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06

Variant links:

Genes affected

OR4C15 (HGNC:15171): (olfactory receptor family 4 subfamily C member 15) 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]

OR4C15 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=-0.88).

BP7

Synonymous conserved (PhyloP=-1.06 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR4C15	NM_001001920.3 linkuse as main transcript	c.267A>G	p.Lys89Lys	synonymous_variant	1/1	ENST00000642128.1	NP_001001920.2	Q8NGM1A0A2C9F2M4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR4C15	ENST00000642128.1 linkuse as main transcript	c.267A>G	p.Lys89Lys	synonymous_variant	1/1		NM_001001920.3	ENSP00000493126.1		Q8NGM1
OR4C15	ENST00000314644.2 linkuse as main transcript	c.429A>G	p.Lys143Lys	synonymous_variant	1/1	6		ENSP00000324958.2		A0A2C9F2M4

Frequencies

GnomAD3 genomes

AF:

0.238

AC:

36137

AN:

151836

Hom.:

4908

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.297

Gnomad AMR

AF:

0.331

Gnomad ASJ

AF:

0.241

Gnomad EAS

AF:

0.363

Gnomad SAS

AF:

0.247

Gnomad FIN

AF:

0.322

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.262

Gnomad OTH

AF:

0.264

GnomAD3 exomes

AF:

0.287

AC:

72053

AN:

250888

Hom.:

11168

AF XY:

0.284

AC XY:

38457

AN XY:

135574

show subpopulations

Gnomad AFR exome

AF:

0.120

Gnomad AMR exome

AF:

0.409

Gnomad ASJ exome

AF:

0.249

Gnomad EAS exome

AF:

0.384

Gnomad SAS exome

AF:

0.244

Gnomad FIN exome

AF:

0.320

Gnomad NFE exome

AF:

0.266

Gnomad OTH exome

AF:

0.300

GnomAD4 exome

AF:

0.265

AC:

386666

AN:

1461530

Hom.:

52959

Cov.:

AF XY:

0.265

AC XY:

192686

AN XY:

727068

show subpopulations

Gnomad4 AFR exome

AF:

0.116

Gnomad4 AMR exome

AF:

0.399

Gnomad4 ASJ exome

AF:

0.250

Gnomad4 EAS exome

AF:

0.357

Gnomad4 SAS exome

AF:

0.246

Gnomad4 FIN exome

AF:

0.313

Gnomad4 NFE exome

AF:

0.259

Gnomad4 OTH exome

AF:

0.266

GnomAD4 genome

AF:

0.238

AC:

36168

AN:

151954

Hom.:

4924

Cov.:

AF XY:

0.241

AC XY:

17935

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.123

Gnomad4 AMR

AF:

0.331

Gnomad4 ASJ

AF:

0.241

Gnomad4 EAS

AF:

0.363

Gnomad4 SAS

AF:

0.248

Gnomad4 FIN

AF:

0.322

Gnomad4 NFE

AF:

0.262

Gnomad4 OTH

AF:

0.273

Alfa

AF:

0.248

Hom.:

2710

Bravo

AF:

0.239

Asia WGS

AF:

0.300

AC:

1042

AN:

3478

EpiCase

AF:

0.280

EpiControl

AF:

0.275

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

4.1

DANN

Benign

0.45

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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