dbSNP rs17316625: OR13H1:p.Leu183Leu (chrX-131544622-C-G) – ACMG Classification: Benign (-13 pts)

Variant summary

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

The NM_001004486.1(OR13H1):c.549C>G(p.Leu183Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 1,207,438 control chromosomes in the GnomAD database, including 46,625 homozygotes. There are 130,590 hemizygotes in GnomAD. 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 ( 3072 hom., 7884 hem., cov: 22)

Exomes 𝑓: 0.34 ( 43553 hom. 122706 hem. )

Consequence

OR13H1
NM_001004486.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.31

Variant links:

Genes affected

OR13H1 (HGNC:14755): (olfactory receptor family 13 subfamily H member 1) 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]

OR13H1 links:

IGSF1 (HGNC:5948): (immunoglobulin superfamily member 1) This gene encodes a member of the immunoglobulin-like domain-containing superfamily. Proteins in this superfamily contain varying numbers of immunoglobulin-like domains and are thought to participate in the regulation of interactions between cells. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2010]

IGSF1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP7

Synonymous conserved (PhyloP=-2.31 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR13H1	NM_001004486.1 link	c.549C>G	p.Leu183Leu	synonymous_variant	Exon 1 of 1	ENST00000338616.6	NP_001004486.1	Q8NG92A0A126GW70

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR13H1	ENST00000338616.6 link	c.549C>G	p.Leu183Leu	synonymous_variant	Exon 1 of 1	6	NM_001004486.1	ENSP00000340748.3		Q8NG92
IGSF1	ENST00000370904.6 link	c.-913+34046G>C		intron_variant	Intron 1 of 26	2		ENSP00000359941.1		Q8N6C5-2

Frequencies

GnomAD3 genomes

AF:

0.243

AC:

26935

AN:

110974

Hom.:

3074

Cov.:

AF XY:

0.237

AC XY:

7877

AN XY:

33190

show subpopulations

Gnomad AFR

AF:

0.0522

Gnomad AMI

AF:

0.415

Gnomad AMR

AF:

0.212

Gnomad ASJ

AF:

0.358

Gnomad EAS

AF:

0.0428

Gnomad SAS

AF:

0.330

Gnomad FIN

AF:

0.321

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.351

Gnomad OTH

AF:

0.254

GnomAD3 exomes

AF:

0.277

AC:

50511

AN:

182641

Hom.:

4969

AF XY:

0.298

AC XY:

20011

AN XY:

67237

show subpopulations

Gnomad AFR exome

AF:

0.0456

Gnomad AMR exome

AF:

0.168

Gnomad ASJ exome

AF:

0.354

Gnomad EAS exome

AF:

0.0440

Gnomad SAS exome

AF:

0.346

Gnomad FIN exome

AF:

0.338

Gnomad NFE exome

AF:

0.353

Gnomad OTH exome

AF:

0.300

GnomAD4 exome

AF:

0.336

AC:

368274

AN:

1096415

Hom.:

43553

Cov.:

AF XY:

0.339

AC XY:

122706

AN XY:

362007

show subpopulations

Gnomad4 AFR exome

AF:

0.0433

Gnomad4 AMR exome

AF:

0.170

Gnomad4 ASJ exome

AF:

0.355

Gnomad4 EAS exome

AF:

0.0527

Gnomad4 SAS exome

AF:

0.347

Gnomad4 FIN exome

AF:

0.334

Gnomad4 NFE exome

AF:

0.362

Gnomad4 OTH exome

AF:

0.311

GnomAD4 genome

AF:

0.243

AC:

26930

AN:

111023

Hom.:

3072

Cov.:

AF XY:

0.237

AC XY:

7884

AN XY:

33249

show subpopulations

Gnomad4 AFR

AF:

0.0521

Gnomad4 AMR

AF:

0.212

Gnomad4 ASJ

AF:

0.358

Gnomad4 EAS

AF:

0.0432

Gnomad4 SAS

AF:

0.331

Gnomad4 FIN

AF:

0.321

Gnomad4 NFE

AF:

0.351

Gnomad4 OTH

AF:

0.255

Alfa

AF:

0.300

Hom.:

2909

Bravo

AF:

0.226

EpiCase

AF:

0.375

EpiControl

AF:

0.376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.3

DANN

Benign

0.58

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