NM_001004482.1:c.243G>C

Variant names:

• chr9-104599171-C-G
• rs75081605
• NM_001004482.1:c.243G>C

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

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
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -3.16
• Publications: 5 publications found

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]

ENSG00000297079 (HGNC:):

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004482.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR13C5	NM_001004482.1	MANE Select	c.243G>C	p.Thr81Thr	synonymous	Exon 1 of 1	NP_001004482.1	Q8NGS8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR13C5	ENST00000374779.3	TSL:6 MANE Select	c.243G>C	p.Thr81Thr	synonymous	Exon 1 of 1	ENSP00000363911.2	Q8NGS8
	ENSG00000297079	ENST00000745188.1		n.370+22859G>C		intron	N/A
	ENSG00000297079	ENST00000745189.1		n.326+22859G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.514 AC: 72838 AN: 141840 Hom.: 18767 Cov.: 29

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

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.: 40 AF XY: 0.451 AC XY: 322036 AN XY: 713472

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

GnomAD4 genome AF: 0.514 AC: 72912 AN: 141952 Hom.: 18785 Cov.: 29 AF XY: 0.518 AC XY: 35955 AN XY: 69352

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

Alfa AF: 0.287 Hom.: 452

ClinVar

ClinVar submissions

Significance: Benign/Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.014
DANN	Benign	0.23
PhyloP100		-3.2
PromoterAI		-0.0090	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs75081605; hg19: chr9-107361452; COSMIC: COSV66164816;