Variant 9-104599158-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001004482.1(OR13C5):c.256C>G(p.Leu86Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 1,581,710 control chromosomes in the GnomAD database, including 177,317 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.52 ( 19332 hom., cov: 29)

Exomes 𝑓: 0.46 ( 157985 hom. )

Consequence

OR13C5
NM_001004482.1 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.09

Variant links:

Genes affected

OR13C5 (HGNC:15100): (olfactory receptor family 13 subfamily C member 5) 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]

OR13C5 links:

LOC107987105 (HGNC:):

LOC107987105 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=7.9223594E-7).

BP6

Variant 9-104599158-G-C is Benign according to our data. Variant chr9-104599158-G-C is described in ClinVar as [Benign]. Clinvar id is 768315.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR13C5	NM_001004482.1 linkuse as main transcript	c.256C>G	p.Leu86Val	missense_variant	1/1	ENST00000374779.3
LOC107987105	XR_007061705.1 linkuse as main transcript	n.427+22872C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR13C5	ENST00000374779.3 linkuse as main transcript	c.256C>G	p.Leu86Val	missense_variant	1/1		NM_001004482.1	P1

Frequencies

GnomAD3 genomes

AF:

0.517

AC:

73586

AN:

142350

Hom.:

19312

Cov.:

show subpopulations

Gnomad AFR

AF:

0.667

Gnomad AMI

AF:

0.434

Gnomad AMR

AF:

0.532

Gnomad ASJ

AF:

0.335

Gnomad EAS

AF:

0.932

Gnomad SAS

AF:

0.530

Gnomad FIN

AF:

0.475

Gnomad MID

AF:

0.365

Gnomad NFE

AF:

0.422

Gnomad OTH

AF:

0.479

GnomAD3 exomes

AF:

0.511

AC:

117773

AN:

230284

Hom.:

32867

AF XY:

0.498

AC XY:

62036

AN XY:

124664

show subpopulations

Gnomad AFR exome

AF:

0.682

Gnomad AMR exome

AF:

0.638

Gnomad ASJ exome

AF:

0.340

Gnomad EAS exome

AF:

0.932

Gnomad SAS exome

AF:

0.512

Gnomad FIN exome

AF:

0.473

Gnomad NFE exome

AF:

0.409

Gnomad OTH exome

AF:

0.454

GnomAD4 exome

AF:

0.464

AC:

668188

AN:

1439246

Hom.:

157985

Cov.:

AF XY:

0.464

AC XY:

332607

AN XY:

716712

show subpopulations

Gnomad4 AFR exome

AF:

0.678

Gnomad4 AMR exome

AF:

0.632

Gnomad4 ASJ exome

AF:

0.342

Gnomad4 EAS exome

AF:

0.957

Gnomad4 SAS exome

AF:

0.522

Gnomad4 FIN exome

AF:

0.481

Gnomad4 NFE exome

AF:

0.432

Gnomad4 OTH exome

AF:

0.468

GnomAD4 genome

AF:

0.517

AC:

73663

AN:

142464

Hom.:

19332

Cov.:

AF XY:

0.522

AC XY:

36355

AN XY:

69654

show subpopulations

Gnomad4 AFR

AF:

0.667

Gnomad4 AMR

AF:

0.532

Gnomad4 ASJ

AF:

0.335

Gnomad4 EAS

AF:

0.932

Gnomad4 SAS

AF:

0.529

Gnomad4 FIN

AF:

0.475

Gnomad4 NFE

AF:

0.422

Gnomad4 OTH

AF:

0.482

Alfa

AF:

0.360

Hom.:

1413

Bravo

AF:

0.567

ExAC

AF:

0.481

AC:

58146

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.74

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0051

Eigen

Benign

-0.81

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.051

LIST_S2

Benign

0.051

MetaRNN

Benign

7.9e-7

MetaSVM

Benign

-0.90

MutationAssessor

Benign

1.5

MutationTaster

Benign

1.0

PrimateAI

Benign

0.24

PROVEAN

Benign

-1.4

REVEL

Benign

0.077

Sift

Benign

0.12

Sift4G

Benign

0.17

Polyphen

0.95

Vest4

0.020

MPC

0.80

ClinPred

0.019

GERP RS

-8.0

Varity_R

0.043

gMVP

0.062

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over