NM_001001921.2:c.-29+982A>C

Variant names:

• chr11-56028694-A-C
• rs2512950
• NM_001001921.2:c.-29+982A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
OR5AS1	NM_001001921.2	c.-29+982A>C		intron_variant	Intron 1 of 1	ENST00000641320.1	NP_001001921.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR5AS1	ENST00000641320.1	c.-29+982A>C		intron_variant	Intron 1 of 1		NM_001001921.2	ENSP00000493325.1

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

African (AFR) AF: 0.395 AC: 16306 AN: 41330

American (AMR) AF: 0.478 AC: 7291 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1329 AN: 3468

East Asian (EAS) AF: 0.608 AC: 3136 AN: 5160

South Asian (SAS) AF: 0.560 AC: 2698 AN: 4818

European-Finnish (FIN) AF: 0.346 AC: 3644 AN: 10542

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24580 AN: 67912

Other (OTH) AF: 0.432 AC: 915 AN: 2116

Alfa AF: 0.385 Hom.: 33200

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
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2512950; hg19: chr11-55796170;