chr1-248039093-T-G

Position:

• chr1-248039093-T-G

Variant summary

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

The NM_001385855.1(OR2L2):​c.826T>G​(p.Phe276Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,461,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.000010 (0 hom.)
• Consequence: OR2L2 NM_001385855.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.523

Genes affected

OR2L2 (HGNC:8266): (olfactory receptor family 2 subfamily L member 2) 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]

OR2L13 (HGNC:):

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=0.31094128).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR2L2	NM_001385855.1	c.826T>G	p.Phe276Val	missense_variant	3/3	ENST00000641771.1
OR2L2	NM_001004686.3	c.826T>G	p.Phe276Val	missense_variant	2/2
OR2L13	NM_001304535.3	c.-18-60265T>G		intron_variant
OR2L13	NM_175911.5	c.-143-59558T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR2L2	ENST00000641771.1	c.826T>G	p.Phe276Val	missense_variant	3/3		NM_001385855.1	P1
OR2L2	ENST00000366479.4	c.826T>G	p.Phe276Val	missense_variant	1/1			P1
OR2L2	ENST00000642011.1	c.826T>G	p.Phe276Val	missense_variant	2/2			P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.0000103 AC: 15 AN: 1461860 Hom.: 0 Cov.: 33 AF XY: 0.0000193 AC XY: 14 AN XY: 727230

Gnomad4 AFR exome AF: 0.000149

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000504

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.0000994

GnomAD4 genome Cov.: 32

ExAC AF: 0.00000824 AC: 1

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

Oct 03, 2022

The c.826T>G (p.F276V) alteration is located in exon 1 (coding exon 1) of the OR2L2 gene. This alteration results from a T to G substitution at nucleotide position 826, causing the phenylalanine (F) at amino acid position 276 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	0.18
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.52
CADD	Benign	19
DANN	Uncertain	0.99
DEOGEN2	Benign	0.013	T;T;T
Eigen	Benign	-0.13
Eigen_PC	Benign	-0.36
FATHMM_MKL	Benign	0.033	N
LIST_S2	Benign	0.71	.;.;T
M_CAP	Benign	0.00076	T
MetaRNN	Benign	0.31	T;T;T
MetaSVM	Benign	-0.94	T
MutationAssessor	Uncertain	2.4	M;M;M
MutationTaster	Benign	0.82	N;N
PrimateAI	Benign	0.25	T
PROVEAN	Pathogenic	-6.1	.;.;D
REVEL	Benign	0.062
Sift	Uncertain	0.010	.;.;D
Sift4G	Uncertain	0.017	.;.;D
Polyphen		0.98	D;D;D
Vest4		0.21
MutPred		0.47		Loss of ubiquitination at K271 (P = 0.0863);Loss of ubiquitination at K271 (P = 0.0863);Loss of ubiquitination at K271 (P = 0.0863);
MVP		0.24
MPC		0.065
ClinPred		0.98	D
GERP RS		1.9
Varity_R		0.34
gMVP		0.11

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: rs376489590; hg19: chr1-248202395; COSMIC: COSV63550761;