rs2512950

Positions:

• chr11-56028694-A-C
• chr11-56028694-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001001921.2(OR5AS1):​c.-29+982A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,794 control chromosomes in the GnomAD database, including 12,453 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 0.40 (12453 hom., cov: 32)
• Consequence: OR5AS1 NM_001001921.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253

Genes affected

OR5AS1 (HGNC:15261): (olfactory receptor family 5 subfamily AS member 1) 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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR5AS1	NM_001001921.2	c.-29+982A>C		intron_variant		ENST00000641320.1	NP_001001921.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR5AS1	ENST00000641320.1	c.-29+982A>C		intron_variant			NM_001001921.2	ENSP00000493325	P1

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60245 AN: 151676 Hom.: 12417 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.397 AC: 60317 AN: 151794 Hom.: 12453 Cov.: 32 AF XY: 0.401 AC XY: 29764 AN XY: 74184

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.432

Alfa AF: 0.382 Hom.: 20618

Bravo AF: 0.407

Asia WGS AF: 0.589 AC: 2045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.5
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2512950; hg19: chr11-55796170;