chr16-3203133-A-G

Variant names:

• chr16-3203133-A-G
• rs224176
• NM_001370640.6:c.-12-1102A>G

Variant summary

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

The NM_012360.3(OR1F1):​c.-12-1102A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0663 in 152,260 control chromosomes in the GnomAD database, including 457 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 0.066 (457 hom., cov: 32)
• Consequence: OR1F1 NM_012360.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428
• Publications: 9 publications found

Genes affected

OR1F1 (HGNC:8194): (olfactory receptor family 1 subfamily F 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0942 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012360.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR1F1	NM_001370640.6	MANE Select	c.-12-1102A>G		intron	N/A	NP_001357569.2
	OR1F1	NM_001370639.4		c.-12-1102A>G		intron	N/A	NP_001357568.2
	OR1F1	NM_001370641.2		c.-252-94A>G		intron	N/A	NP_001357570.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR1F1	ENST00000304646.3	TSL:6 MANE Select	c.-12-1102A>G		intron	N/A	ENSP00000305424.2
	OR1F1	ENST00000903483.1		c.-12-1102A>G		intron	N/A	ENSP00000573542.1
	OR1F1	ENST00000938262.1		c.-12-1102A>G		intron	N/A	ENSP00000608321.1

Frequencies

GnomAD3 genomes AF: 0.0664 AC: 10095 AN: 152142 Hom.: 458 Cov.: 32

Gnomad AFR AF: 0.0239

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0601

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0352

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0962

Gnomad OTH AF: 0.0741

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0663 AC: 10091 AN: 152260 Hom.: 457 Cov.: 32 AF XY: 0.0649 AC XY: 4832 AN XY: 74438

African (AFR) AF: 0.0239 AC: 992 AN: 41566

American (AMR) AF: 0.0599 AC: 916 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 182 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5182

South Asian (SAS) AF: 0.0356 AC: 172 AN: 4830

European-Finnish (FIN) AF: 0.100 AC: 1060 AN: 10590

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0962 AC: 6539 AN: 68006

Other (OTH) AF: 0.0733 AC: 155 AN: 2114

Alfa AF: 0.0826 Hom.: 1034

Bravo AF: 0.0608

Asia WGS AF: 0.0180 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.1
DANN	Benign	0.29
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs224176; hg19: chr16-3253133;