rs7753474

Variant names:

• chr6-29373531-G-A
• rs7753474
• NM_030959.3:c.*806C>T

Variant summary

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

The NM_030959.3(OR12D3):​c.*806C>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 0.223 in 152,512 control chromosomes in the GnomAD database, including 3,901 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 0.22 (3889 hom., cov: 32)
  • Exomes 𝑓: 0.20 (12 hom.)
• Consequence: OR12D3 NM_030959.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647
• Publications: 14 publications found

Genes affected

OR12D3 (HGNC:13963): (olfactory receptor family 12 subfamily D member 3) 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]

OR5V1 (HGNC:13972): (olfactory receptor family 5 subfamily V 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=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR12D3	NM_030959.3	c.*806C>T		3_prime_UTR_variant	Exon 1 of 1	ENST00000396806.3	NP_112221.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR12D3	ENST00000396806.3	c.*806C>T		3_prime_UTR_variant	Exon 1 of 1	6	NM_030959.3	ENSP00000380023.3
OR5V1	ENST00000377154.1	c.-82-17254C>T		intron_variant	Intron 3 of 3	6		ENSP00000366359.1

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33869 AN: 151850 Hom.: 3883 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.232

GnomAD4 exome AF: 0.202 AC: 110 AN: 544 Hom.: 12 Cov.: 0 AF XY: 0.232 AC XY: 64 AN XY: 276

African (AFR) AF: 0.231 AC: 6 AN: 26

American (AMR) AF: 0.250 AC: 3 AN: 12

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 12 AN: 22

East Asian (EAS) AF: 0.333 AC: 2 AN: 6

South Asian (SAS) AF: 0.375 AC: 3 AN: 8

European-Finnish (FIN) AF: 0.167 AC: 3 AN: 18

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.170 AC: 72 AN: 424

Other (OTH) AF: 0.308 AC: 8 AN: 26

GnomAD4 genome AF: 0.223 AC: 33894 AN: 151968 Hom.: 3889 Cov.: 32 AF XY: 0.225 AC XY: 16681 AN XY: 74250

African (AFR) AF: 0.275 AC: 11412 AN: 41456

American (AMR) AF: 0.222 AC: 3394 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1081 AN: 3464

East Asian (EAS) AF: 0.240 AC: 1246 AN: 5184

South Asian (SAS) AF: 0.235 AC: 1134 AN: 4820

European-Finnish (FIN) AF: 0.203 AC: 2140 AN: 10542

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12801 AN: 67932

Other (OTH) AF: 0.232 AC: 489 AN: 2104

Alfa AF: 0.204 Hom.: 9801

Bravo AF: 0.230

Asia WGS AF: 0.251 AC: 870 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	0.82
DANN	Benign	0.33
PhyloP100		-0.65
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7753474; hg19: chr6-29341308;