11-56703892-C-T

Variant names:

• chr11-56703892-C-T
• rs637404
• NM_001005213.2:c.*2587C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001005213.2(OR9G1):​c.*2587C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. 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 0.73 (35392 hom., cov: 56)
  • Failed GnomAD Quality Control
• Consequence: OR9G1 NM_001005213.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 0 publications found

Genes affected

OR9G1 (HGNC:15319): (olfactory receptor family 9 subfamily G 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]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR9G1	NM_001005213.2	c.*2587C>T		downstream_gene_variant		ENST00000642097.1	NP_001005213.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR9G1	ENST00000642097.1	c.*2587C>T		downstream_gene_variant			NM_001005213.2	ENSP00000493255.1

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111385 AN: 152062 Hom.: 35356 Cov.: 56

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.728

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.733 AC: 111480 AN: 152180 Hom.: 35392 Cov.: 56 AF XY: 0.736 AC XY: 54745 AN XY: 74414

African (AFR) AF: 0.729 AC: 30277 AN: 41524

American (AMR) AF: 0.776 AC: 11865 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2485 AN: 3470

East Asian (EAS) AF: 0.848 AC: 4396 AN: 5186

South Asian (SAS) AF: 0.787 AC: 3798 AN: 4824

European-Finnish (FIN) AF: 0.751 AC: 7965 AN: 10602

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48320 AN: 67976

Other (OTH) AF: 0.730 AC: 1541 AN: 2112

Alfa AF: 0.704 Hom.: 1281

Asia WGS AF: 0.780 AC: 2700 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.17
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs637404; hg19: chr11-56471368;