chr11-6002646-C-A

Variant names:

• chr11-6002646-C-A
• rs1303556263
• NM_001005179.4:c.347G>T

Variant summary

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

The NM_001005179.4(OR56A4):​c.347G>T​(p.Cys116Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,890 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: 6.8e-7 (0 hom.)
• Consequence: OR56A4 NM_001005179.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.254

Genes affected

OR56A4 (HGNC:14791): (olfactory receptor family 56 subfamily A member 4) 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]

OR56A3 (HGNC:14786): (olfactory receptor family 56 subfamily A member 3) 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=0.09439704).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR56A4	NM_001005179.4	c.347G>T	p.Cys116Phe	missense_variant	Exon 3 of 3	ENST00000641156.1	NP_001005179.3
OR56A3	XM_047426926.1	c.*469-1074C>A		intron_variant	Intron 3 of 5		XP_047282882.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR56A4	ENST00000641156.1	c.347G>T	p.Cys116Phe	missense_variant	Exon 3 of 3		NM_001005179.4	ENSP00000492932.1
OR56A4	ENST00000330728.4	c.503G>T	p.Cys168Phe	missense_variant	Exon 1 of 1	6		ENSP00000328215.4
OR56A4	ENST00000641279.1	c.347G>T	p.Cys116Phe	missense_variant	Exon 1 of 1			ENSP00000492934.1
OR56A4	ENST00000641835.1	c.347G>T	p.Cys116Phe	missense_variant	Exon 2 of 2			ENSP00000493371.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461890 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 727244

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Mar 01, 2025

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.503G>T (p.C168F) alteration is located in exon 1 (coding exon 1) of the OR56A4 gene. This alteration results from a G to T substitution at nucleotide position 503, causing the cysteine (C) at amino acid position 168 to be replaced by a phenylalanine (F). 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	Uncertain	0.35
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	19
DANN	Uncertain	0.99
DEOGEN2	Benign	0.12	T;T;T;.
Eigen	Benign	-0.47
Eigen_PC	Benign	-0.53
FATHMM_MKL	Benign	0.056	N
LIST_S2	Uncertain	0.91	.;.;D;D
M_CAP	Benign	0.0041	T
MetaRNN	Benign	0.094	T;T;T;T
MetaSVM	Benign	-0.87	T
MutationAssessor	Benign	-0.96	N;N;N;.
PrimateAI	Benign	0.23	T
PROVEAN	Uncertain	-3.5	.;.;.;D
REVEL	Benign	0.090
Sift	Benign	0.068	.;.;.;T
Sift4G	Benign	0.56	.;.;.;T
Polyphen		0.74	P;P;P;.
Vest4		0.18
MutPred		0.54		Loss of catalytic residue at M119 (P = 0.3583);Loss of catalytic residue at M119 (P = 0.3583);Loss of catalytic residue at M119 (P = 0.3583);.;
MVP		0.19
MPC		0.18
ClinPred		0.42	T
GERP RS		2.6
Varity_R		0.26
gMVP		0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs1303556263; hg19: chr11-6023876;