11-59515087-A-G

Variant names:

• chr11-59515087-A-G
• NM_001004711.2:c.175A>G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001004711.2(OR4D9):​c.175A>G​(p.Met59Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: OR4D9 NM_001004711.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 5.14

Genes affected

OR4D9 (HGNC:15178): (olfactory receptor family 4 subfamily D member 9) 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 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.40747374).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR4D9	NM_001004711.2	c.175A>G	p.Met59Val	missense_variant	Exon 3 of 3	ENST00000641962.1	NP_001004711.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR4D9	ENST00000641962.1	c.175A>G	p.Met59Val	missense_variant	Exon 3 of 3		NM_001004711.2	ENSP00000493010.1
OR4D9	ENST00000641278.1	c.175A>G	p.Met59Val	missense_variant	Exon 3 of 3			ENSP00000493042.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jun 28, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.175A>G (p.M59V) alteration is located in exon 1 (coding exon 1) of the OR4D9 gene. This alteration results from a A to G substitution at nucleotide position 175, causing the methionine (M) at amino acid position 59 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.44
CADD	Benign	22
DANN	Benign	0.94
DEOGEN2	Benign	0.011	T;T;T
Eigen	Uncertain	0.26
Eigen_PC	Benign	0.11
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Benign	0.76	.;.;T
M_CAP	Benign	0.0060	T
MetaRNN	Benign	0.41	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Pathogenic	3.5	H;H;H
PrimateAI	Benign	0.22	T
PROVEAN	Uncertain	-3.6	.;.;D
REVEL	Benign	0.095
Sift	Uncertain	0.014	.;.;D
Sift4G	Pathogenic	0.0010	.;.;D
Polyphen		0.82	P;P;P
Vest4		0.43
MutPred		0.27		Gain of methylation at R64 (P = 0.3327);Gain of methylation at R64 (P = 0.3327);Gain of methylation at R64 (P = 0.3327);
MVP		0.47
MPC		0.095
ClinPred		0.95	D
GERP RS		1.7
Varity_R		0.52
gMVP		0.11

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: chr11-59282560; COSMIC: COSV100260063;