rs80227456

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001004482.1(OR13C5):c.244C>T(p.Leu82Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 142,032 control chromosomes in the GnomAD database, including 18,776 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.51 ( 18776 hom., cov: 28)

Exomes 𝑓: 0.45 ( 142549 hom. )

Failed GnomAD Quality Control

Consequence

OR13C5
NM_001004482.1 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.03

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 9-104599170-G-A is Benign according to our data. Variant chr9-104599170-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 403269.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.03 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR13C5	NM_001004482.1 link	c.244C>T	p.Leu82Leu	synonymous_variant	Exon 1 of 1	ENST00000374779.3	NP_001004482.1	Q8NGS8
LOC107987105	XR_007061705.1 link	n.427+22860C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR13C5	ENST00000374779.3 link	c.244C>T	p.Leu82Leu	synonymous_variant	Exon 1 of 1	6	NM_001004482.1	ENSP00000363911.2		Q8NGS8

Frequencies

GnomAD3 genomes

AF:

0.513

AC:

72829

AN:

141916

Hom.:

18758

Cov.:

show subpopulations

Gnomad AFR

AF:

0.660

Gnomad AMI

AF:

0.436

Gnomad AMR

AF:

0.529

Gnomad ASJ

AF:

0.334

Gnomad EAS

AF:

0.924

Gnomad SAS

AF:

0.527

Gnomad FIN

AF:

0.471

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.420

Gnomad OTH

AF:

0.473

GnomAD3 exomes

AF:

0.475

AC:

96815

AN:

203832

Hom.:

26738

AF XY:

0.460

AC XY:

50421

AN XY:

109684

show subpopulations

Gnomad AFR exome

AF:

0.629

Gnomad AMR exome

AF:

0.615

Gnomad ASJ exome

AF:

0.311

Gnomad EAS exome

AF:

0.910

Gnomad SAS exome

AF:

0.463

Gnomad FIN exome

AF:

0.450

Gnomad NFE exome

AF:

0.371

Gnomad OTH exome

AF:

0.422

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.454

AC:

652646

AN:

1439004

Hom.:

142549

Cov.:

AF XY:

0.454

AC XY:

325276

AN XY:

716400

show subpopulations

Gnomad4 AFR exome

AF:

0.632

Gnomad4 AMR exome

AF:

0.623

Gnomad4 ASJ exome

AF:

0.340

Gnomad4 EAS exome

AF:

0.924

Gnomad4 SAS exome

AF:

0.513

Gnomad4 FIN exome

AF:

0.478

Gnomad4 NFE exome

AF:

0.422

Gnomad4 OTH exome

AF:

0.458

GnomAD4 genome

AF:

0.513

AC:

72904

AN:

142032

Hom.:

18776

Cov.:

AF XY:

0.518

AC XY:

35942

AN XY:

69396

show subpopulations

Gnomad4 AFR

AF:

0.660

Gnomad4 AMR

AF:

0.529

Gnomad4 ASJ

AF:

0.334

Gnomad4 EAS

AF:

0.923

Gnomad4 SAS

AF:

0.526

Gnomad4 FIN

AF:

0.471

Gnomad4 NFE

AF:

0.420

Gnomad4 OTH

AF:

0.476

Alfa

AF:

0.509

Hom.:

2164

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Dec 31, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.1

DANN

Benign

0.50

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.16

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