chr11-6002076-A-G

Position:

• chr11-6002076-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_001005179.4(OR56A4):​c.917T>C​(p.Ile306Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000346 in 1,445,246 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000035 (0 hom.)
• Consequence: OR56A4 NM_001005179.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.40

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 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.817

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR56A4	NM_001005179.4	c.917T>C	p.Ile306Thr	missense_variant	3/3	ENST00000641156.1	NP_001005179.3
OR56A3	XM_047426926.1	c.*469-1644A>G		intron_variant			XP_047282882.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR56A4	ENST00000641156.1	c.917T>C	p.Ile306Thr	missense_variant	3/3		NM_001005179.4	ENSP00000492932.1
OR56A4	ENST00000330728.4	c.1073T>C	p.Ile358Thr	missense_variant	1/1	6		ENSP00000328215.4
OR56A4	ENST00000641279.1	c.917T>C	p.Ile306Thr	missense_variant	1/1			ENSP00000492934.1
OR56A4	ENST00000641835.1	c.917T>C	p.Ile306Thr	missense_variant	2/2			ENSP00000493371.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.00000421 AC: 1 AN: 237344 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 127678

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000550

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000346 AC: 5 AN: 1445246 Hom.: 0 Cov.: 31 AF XY: 0.00000139 AC XY: 1 AN XY: 717312

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000253

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000670

GnomAD4 genome Cov.: 33

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 04, 2024

The c.1073T>C (p.I358T) alteration is located in exon 1 (coding exon 1) of the OR56A4 gene. This alteration results from a T to C substitution at nucleotide position 1073, causing the isoleucine (I) at amino acid position 358 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	Pathogenic	0.65
BayesDel_addAF	Uncertain	0.060	T
BayesDel_noAF	Benign	-0.15
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Benign	0.11	T;T;T;.
Eigen	Benign	0.16
Eigen_PC	Benign	0.036
FATHMM_MKL	Benign	0.71	D
LIST_S2	Uncertain	0.93	.;.;D;D
M_CAP	Benign	0.010	T
MetaRNN	Pathogenic	0.82	D;D;D;D
MetaSVM	Benign	-0.42	T
MutationAssessor	Pathogenic	3.2	M;M;M;.
PrimateAI	Benign	0.44	T
PROVEAN	Uncertain	-3.1	.;.;.;D
REVEL	Benign	0.21
Sift	Uncertain	0.0010	.;.;.;D
Sift4G	Uncertain	0.0040	.;.;.;D
Polyphen		0.73	P;P;P;.
Vest4		0.65
MutPred		0.80		Gain of disorder (P = 0.0133);Gain of disorder (P = 0.0133);Gain of disorder (P = 0.0133);.;
MVP		0.67
MPC		0.22
ClinPred		0.99	D
GERP RS		4.2
Varity_R		0.19
gMVP		0.29

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: rs769516592; hg19: chr11-6023306;