chr11-4955504-C-A

Position:

• chr11-4955504-C-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001004748.1(OR51A2):​c.210G>T​(p.Met70Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.000091 (0 hom., cov: 17)
  • Exomes 𝑓: 0.000082 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: OR51A2 NM_001004748.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -5.22

Genes affected

OR51A2 (HGNC:14764): (olfactory receptor family 51 subfamily A 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]

MMP26 (HGNC:14249): (matrix metallopeptidase 26) Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. The encoded preproprotein is proteolytically processed to generate the mature enzyme. This enzyme may degrade collagen type IV, fibronectin, fibrinogen, and beta-casein, and activate matrix metalloproteinase-9 by cleavage. The protein differs from most MMP family members in that it lacks a conserved C-terminal protein domain. The encoded protein may promote cell invasion in multiple human cancers. [provided by RefSeq, May 2016]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.028194845).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR51A2	NM_001004748.1	c.210G>T	p.Met70Ile	missense_variant	1/1	ENST00000380371.1
MMP26	NM_021801.5	c.-144-32564C>A		intron_variant		ENST00000380390.6
MMP26	NM_001384608.1	c.-152-32766C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR51A2	ENST00000380371.1	c.210G>T	p.Met70Ile	missense_variant	1/1		NM_001004748.1	P1
MMP26	ENST00000380390.6	c.-144-32564C>A		intron_variant		5	NM_021801.5	P1
MMP26	ENST00000300762.2	c.-152-32766C>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 11 AN: 120756 Hom.: 0 Cov.: 17 FAILED QC

Gnomad AFR AF: 0.0000288

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000178

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000148

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000825 AC: 98 AN: 1188394 Hom.: 0 Cov.: 31 AF XY: 0.0000704 AC XY: 42 AN XY: 596750

Gnomad4 AFR exome AF: 0.0000674

Gnomad4 AMR exome AF: 0.000370

Gnomad4 ASJ exome AF: 0.0000441

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000891

Gnomad4 OTH exome AF: 0.0000583

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000910 AC: 11 AN: 120874 Hom.: 0 Cov.: 17 AF XY: 0.0000854 AC XY: 5 AN XY: 58552

Gnomad4 AFR AF: 0.0000287

Gnomad4 AMR AF: 0.000178

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000148

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000241 Hom.: 0

ExAC AF: 0.000111 AC: 13

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

Jun 24, 2022

The c.210G>T (p.M70I) alteration is located in exon 1 (coding exon 1) of the OR51A2 gene. This alteration results from a G to T substitution at nucleotide position 210, causing the methionine (M) at amino acid position 70 to be replaced by an isoleucine (I). 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	0.14
BayesDel_addAF	Benign	-0.38	T
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.0020
DANN	Benign	0.63
DEOGEN2	Benign	0.00036	T
Eigen	Benign	-1.9
Eigen_PC	Benign	-1.9
FATHMM_MKL	Benign	0.0045	N
LIST_S2	Benign	0.58	T
M_CAP	Benign	0.0050	T
MetaRNN	Benign	0.028	T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	-1.5	N
MutationTaster	Benign	0.99	D;N
PROVEAN	Benign	0.41	N
REVEL	Benign	0.010
Sift	Benign	0.27	T
Sift4G	Benign	0.35	T
Polyphen		0.0	B
Vest4		0.026
MutPred		0.24		Loss of disorder (P = 0.0786);
MVP		0.27
MPC		1.2
ClinPred		0.034	T
GERP RS		-5.4
Varity_R		0.059
gMVP		0.13

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs753764563; hg19: chr11-4976734;