chr9-122750380-T-A

Position:

• chr9-122750380-T-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001004453.3(OR1L6):​c.533T>A​(p.Phe178Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 22)
• Consequence: OR1L6 NM_001004453.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.376

Genes affected

OR1L6 (HGNC:8218): (olfactory receptor family 1 subfamily L member 6) 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 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2601435).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR1L6	NM_001004453.3	c.533T>A	p.Phe178Tyr	missense_variant	2/2	ENST00000304720.3	NP_001004453.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR1L6	ENST00000304720.3	c.533T>A	p.Phe178Tyr	missense_variant	2/2	6	NM_001004453.3	ENSP00000304235.2
OR1L6	ENST00000373684.1	c.641T>A	p.Phe214Tyr	missense_variant	1/1	6		ENSP00000362788.1

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 22

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 03, 2024

The c.533T>A (p.F178Y) alteration is located in exon 1 (coding exon 1) of the OR1L6 gene. This alteration results from a T to A substitution at nucleotide position 533, causing the phenylalanine (F) at amino acid position 178 to be replaced by a tyrosine (Y). 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	0.16
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Benign	-0.51
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.014	.;T
Eigen	Uncertain	0.20
Eigen_PC	Benign	0.079
FATHMM_MKL	Benign	0.36	N
LIST_S2	Benign	0.62	T;T
M_CAP	Benign	0.0017	T
MetaRNN	Benign	0.26	T;T
MetaSVM	Benign	-0.95	T
MutationAssessor	Uncertain	2.3	.;M
PrimateAI	Benign	0.28	T
PROVEAN	Uncertain	-2.7	D;D
REVEL	Benign	0.12
Sift	Benign	0.053	T;T
Sift4G	Uncertain	0.036	D;T
Polyphen		1.0	.;D
Vest4		0.27
MutPred		0.60		.;Loss of stability (P = 0.0853);
MVP		0.53
MPC		0.37
ClinPred		0.94	D
GERP RS		3.4
Varity_R		0.36
gMVP		0.056

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

LitVar

Other links and lift over

dbSNP: rs1828881580; hg19: chr9-125512659;