rs2499949

Variant names:

• chr11-5130286-G-A
• rs2499949
• NM_001005160.3:c.*1406C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-5130286-G-A
• chr11-5130286-G-T

Variant summary

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

The NM_001005160.3(OR52A5):​c.*1406C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 151,670 control chromosomes in the GnomAD database, including 2,837 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 0.17 (2837 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: OR52A5 NM_001005160.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 1 publications found

Genes affected

OR52A5 (HGNC:19580): (olfactory receptor family 52 subfamily A member 5) 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR52A5	NM_001005160.3	c.*1406C>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000307388.2	NP_001005160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR52A5	ENST00000307388.2	c.*1406C>T		3_prime_UTR_variant	Exon 2 of 2	6	NM_001005160.3	ENSP00000303469.1
OR52A5	ENST00000642125.1	c.*1406C>T		3_prime_UTR_variant	Exon 2 of 2			ENSP00000493298.1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26134 AN: 151546 Hom.: 2833 Cov.: 32

Gnomad AFR AF: 0.0471

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.107

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.168

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.172 AC: 26143 AN: 151670 Hom.: 2837 Cov.: 32 AF XY: 0.176 AC XY: 13003 AN XY: 74082

African (AFR) AF: 0.0469 AC: 1941 AN: 41390

American (AMR) AF: 0.208 AC: 3171 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 528 AN: 3462

East Asian (EAS) AF: 0.371 AC: 1911 AN: 5146

South Asian (SAS) AF: 0.233 AC: 1118 AN: 4804

European-Finnish (FIN) AF: 0.212 AC: 2225 AN: 10494

Middle Eastern (MID) AF: 0.106 AC: 30 AN: 284

European-Non Finnish (NFE) AF: 0.218 AC: 14779 AN: 67844

Other (OTH) AF: 0.172 AC: 363 AN: 2106

Alfa AF: 0.205 Hom.: 2419

Bravo AF: 0.166

Asia WGS AF: 0.315 AC: 1082 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.47
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2499949; hg19: chr11-5151516;