rs1320892

chr7-144055135-G-A

Variant summary

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

The NM_012365.2(OR2A5):c.*3798G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,134 control chromosomes in the GnomAD database, including 5,514 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 0.24 (5514 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: OR2A5 NM_012365.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500

Genes affected

OR2A5 (HGNC:8232): (olfactory receptor family 2 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

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 = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR2A5	NM_012365.2	c.*3798G>A		3_prime_UTR_variant	2/2	ENST00000641693.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR2A5	ENST00000641693.1	c.*3798G>A		3_prime_UTR_variant	2/2		NM_012365.2	P1
OR2A5	ENST00000641779.1	n.187-3333G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36904 AN: 152016 Hom.: 5490 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.243 AC: 36969 AN: 152134 Hom.: 5514 Cov.: 33 AF XY: 0.254 AC XY: 18864 AN XY: 74352

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.263

Alfa AF: 0.228 Hom.: 8901

Bravo AF: 0.257

Asia WGS AF: 0.443 AC: 1539 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	1.8
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1320892; hg19: chr7-143752228;