9-104599171-C-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001004482.1(OR13C5):c.243G>C(p.Thr81Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 141,952 control chromosomes in the GnomAD database, including 18,785 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T81T) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.51 ( 18785 hom., cov: 29)

Exomes 𝑓: 0.45 ( 138694 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: -3.16

Publications

5 publications found

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:

ENSG00000297079 (HGNC:):

ENSG00000297079 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

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

BP6

Variant 9-104599171-C-G is Benign according to our data. Variant chr9-104599171-C-G is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 403270.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.16 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR13C5	NM_001004482.1 link	c.243G>C	p.Thr81Thr	synonymous_variant	Exon 1 of 1	ENST00000374779.3	NP_001004482.1
LOC107987105	XR_007061705.1 link	n.427+22859G>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR13C5	ENST00000374779.3 link	c.243G>C	p.Thr81Thr	synonymous_variant	Exon 1 of 1	6	NM_001004482.1	ENSP00000363911.2

Frequencies

GnomAD3 genomes

AF:

0.514

AC:

72838

AN:

141840

Hom.:

18767

Cov.:

show subpopulations

Gnomad AFR

AF:

0.660

Gnomad AMI

AF:

0.434

Gnomad AMR

AF:

0.530

Gnomad ASJ

AF:

0.332

Gnomad EAS

AF:

0.923

Gnomad SAS

AF:

0.528

Gnomad FIN

AF:

0.472

Gnomad MID

AF:

0.359

Gnomad NFE

AF:

0.420

Gnomad OTH

AF:

0.473

GnomAD2 exomes

AF:

0.473

AC:

96267

AN:

203342

AF XY:

0.458

show subpopulations

Gnomad AFR exome

AF:

0.629

Gnomad AMR exome

AF:

0.613

Gnomad ASJ exome

AF:

0.312

Gnomad EAS exome

AF:

0.908

Gnomad FIN exome

AF:

0.449

Gnomad NFE exome

AF:

0.370

Gnomad OTH exome

AF:

0.422

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.451

AC:

645566

AN:

1432566

Hom.:

138694

Cov.:

AF XY:

0.451

AC XY:

322036

AN XY:

713472

show subpopulations

African (AFR)

AF:

0.626

AC:

19900

AN:

31792

American (AMR)

AF:

0.622

AC:

27275

AN:

43832

Ashkenazi Jewish (ASJ)

AF:

0.339

AC:

8790

AN:

25954

East Asian (EAS)

AF:

0.924

AC:

35753

AN:

38710

South Asian (SAS)

AF:

0.511

AC:

43304

AN:

84726

European-Finnish (FIN)

AF:

0.478

AC:

25382

AN:

53130

Middle Eastern (MID)

AF:

0.320

AC:

1832

AN:

5724

European-Non Finnish (NFE)

AF:

0.419

AC:

456394

AN:

1089492

Other (OTH)

AF:

0.455

AC:

26936

AN:

59206

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.454

Heterozygous variant carriers

17447

34894

52340

69787

87234

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14594

29188

43782

58376

72970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.514

AC:

72912

AN:

141952

Hom.:

18785

Cov.:

AF XY:

0.518

AC XY:

35955

AN XY:

69352

show subpopulations

African (AFR)

AF:

0.660

AC:

23963

AN:

36288

American (AMR)

AF:

0.530

AC:

7637

AN:

14418

Ashkenazi Jewish (ASJ)

AF:

0.332

AC:

1134

AN:

3412

East Asian (EAS)

AF:

0.922

AC:

3964

AN:

4298

South Asian (SAS)

AF:

0.527

AC:

2367

AN:

4494

European-Finnish (FIN)

AF:

0.472

AC:

4765

AN:

10088

Middle Eastern (MID)

AF:

0.359

AC:

104

AN:

290

European-Non Finnish (NFE)

AF:

0.420

AC:

27633

AN:

65760

Other (OTH)

AF:

0.476

AC:

961

AN:

2020

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

1411

2822

4232

5643

7054

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

652

1304

1956

2608

3260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.287

Hom.:

452

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

0.014

(source)

DANN

Benign

0.23

PhyloP100

-3.2

PromoterAI

-0.0090

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over