rs17480

Variant names:

• chr11-6004881-G-A
• rs17480
• NM_001005179.4:c.-37+1368C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001005179.4(OR56A4):​c.-37+1368C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,916 control chromosomes in the GnomAD database, including 20,440 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.51 (20440 hom., cov: 32)
• Consequence: OR56A4 NM_001005179.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.788
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR56A4	NM_001005179.4	c.-37+1368C>T		intron_variant	Intron 2 of 2	ENST00000641156.1	NP_001005179.3
OR56A3	XM_047426926.1	c.*679+370G>A		intron_variant	Intron 5 of 5		XP_047282882.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR56A4	ENST00000641156.1	c.-37+1368C>T		intron_variant	Intron 2 of 2		NM_001005179.4	ENSP00000492932.1
OR56A4	ENST00000641835.1	c.-36-1853C>T		intron_variant	Intron 1 of 1			ENSP00000493371.1

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76993 AN: 151798 Hom.: 20437 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.522

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.507 AC: 77016 AN: 151916 Hom.: 20440 Cov.: 32 AF XY: 0.506 AC XY: 37582 AN XY: 74256

African (AFR) AF: 0.380 AC: 15707 AN: 41366

American (AMR) AF: 0.463 AC: 7074 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2132 AN: 3468

East Asian (EAS) AF: 0.361 AC: 1869 AN: 5176

South Asian (SAS) AF: 0.716 AC: 3453 AN: 4820

European-Finnish (FIN) AF: 0.506 AC: 5331 AN: 10528

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39719 AN: 67960

Other (OTH) AF: 0.520 AC: 1099 AN: 2114

Alfa AF: 0.553 Hom.: 38881

Bravo AF: 0.491

Asia WGS AF: 0.554 AC: 1923 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.60
DANN	Benign	0.22
PhyloP100		-0.79

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17480; hg19: chr11-6026111;