11-56743106-T-G

Variant names:

• chr11-56743106-T-G
• NM_001005284.2:c.661A>C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001005284.2(OR9G4):​c.661A>C​(p.Ile221Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,876 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: OR9G4 NM_001005284.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.66

Genes affected

OR9G4 (HGNC:15322): (olfactory receptor family 9 subfamily G member 4) 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

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR9G4	NM_001005284.2	c.661A>C	p.Ile221Leu	missense_variant	Exon 2 of 2	ENST00000641668.1	NP_001005284.2
OR9G4	NM_001390832.1	c.661A>C	p.Ile221Leu	missense_variant	Exon 2 of 2		NP_001377761.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR9G4	ENST00000641668.1	c.661A>C	p.Ile221Leu	missense_variant	Exon 2 of 2		NM_001005284.2	ENSP00000493182.1
OR9G4	ENST00000641581.1	c.661A>C	p.Ile221Leu	missense_variant	Exon 2 of 2			ENSP00000493212.1
OR9G4	ENST00000641505.1	n.647A>C		non_coding_transcript_exon_variant	Exon 2 of 2
OR9G4	ENST00000641980.1	n.644A>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461876 Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1 AN XY: 727242

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.38
BayesDel_addAF	Benign	-0.077	T
BayesDel_noAF	Benign	-0.35
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.014	.;.;T
Eigen	Pathogenic	0.68
Eigen_PC	Uncertain	0.55
FATHMM_MKL	Uncertain	0.82	D
LIST_S2	Benign	0.74	.;T;T
M_CAP	Benign	0.0026	T
MetaRNN	Uncertain	0.49	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Pathogenic	3.6	.;.;H
PrimateAI	Benign	0.36	T
PROVEAN	Benign	-2.0	.;.;N
REVEL	Benign	0.20
Sift	Uncertain	0.0010	.;.;D
Sift4G	Uncertain	0.0020	.;.;D
Polyphen		0.99	.;.;D
Vest4		0.53
MutPred		0.64		.;.;Gain of catalytic residue at I236 (P = 0.0643);
MVP		0.58
MPC		0.021
ClinPred		0.97	D
GERP RS		5.1
Varity_R		0.64
gMVP		0.18

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-56510582;