chr11-59422440-G-T

Position:

• chr11-59422440-G-T

Variant summary

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

The NM_001001954.2(OR5A2):​c.514C>A​(p.Pro172Thr) 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. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P172L) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: OR5A2 NM_001001954.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.717

Genes affected

OR5A2 (HGNC:15249): (olfactory receptor family 5 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]

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=0.25905353).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR5A2	NM_001001954.2	c.514C>A	p.Pro172Thr	missense_variant	2/2	ENST00000302040.6	NP_001001954.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR5A2	ENST00000302040.6	c.514C>A	p.Pro172Thr	missense_variant	2/2	6	NM_001001954.2	ENSP00000303834.4
OR5A2	ENST00000641361.1	c.514C>A	p.Pro172Thr	missense_variant	2/2			ENSP00000493065.1
OR5A2	ENST00000641673.1	c.514C>A	p.Pro172Thr	missense_variant	1/1			ENSP00000492975.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

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

Jan 03, 2024

The c.514C>A (p.P172T) alteration is located in exon 1 (coding exon 1) of the OR5A2 gene. This alteration results from a C to A substitution at nucleotide position 514, causing the proline (P) at amino acid position 172 to be replaced by a threonine (T). 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	0.15
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Benign	0.011	T;T;T
Eigen	Benign	0.11
Eigen_PC	Benign	-0.047
FATHMM_MKL	Benign	0.38	N
LIST_S2	Benign	0.80	.;.;T
M_CAP	Benign	0.0045	T
MetaRNN	Benign	0.26	T;T;T
MetaSVM	Benign	-0.93	T
MutationAssessor	Uncertain	2.1	M;M;M
PrimateAI	Benign	0.23	T
PROVEAN	Pathogenic	-5.5	D;.;.
REVEL	Benign	0.054
Sift	Uncertain	0.013	D;.;.
Sift4G	Benign	0.18	T;.;.
Polyphen		0.99	D;D;D
Vest4		0.43
MutPred		0.38		Gain of catalytic residue at P172 (P = 0.0085);Gain of catalytic residue at P172 (P = 0.0085);Gain of catalytic residue at P172 (P = 0.0085);
MVP		0.51
MPC		0.21
ClinPred		0.97	D
GERP RS		3.5
Varity_R		0.51
gMVP		0.11

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: chr11-59189913;