rs1320892

Variant names:

• chr7-144055135-G-A
• rs1320892
• NM_012365.2:c.*3798G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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

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 = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR2A5	NM_012365.2	c.*3798G>A		3_prime_UTR_variant	Exon 2 of 2	ENST00000641693.1	NP_036497.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR2A5	ENST00000641693.1	c.*3798G>A		3_prime_UTR_variant	Exon 2 of 2		NM_012365.2	ENSP00000493295.1
OR2A5	ENST00000641779.1	n.187-3333G>A		intron_variant	Intron 1 of 1

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

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

African (AFR) AF: 0.163 AC: 6758 AN: 41526

American (AMR) AF: 0.436 AC: 6660 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 691 AN: 3470

East Asian (EAS) AF: 0.660 AC: 3405 AN: 5162

South Asian (SAS) AF: 0.260 AC: 1253 AN: 4820

European-Finnish (FIN) AF: 0.292 AC: 3082 AN: 10566

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14446 AN: 67992

Other (OTH) AF: 0.263 AC: 555 AN: 2114

Alfa AF: 0.230 Hom.: 19484

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
PhyloP100		0.050

Splicing

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

Other links and lift over

dbSNP: rs1320892; hg19: chr7-143752228;