12-55638053-A-G

Variant names:

• chr12-55638053-A-G
• rs7309433
• ENST00000715996.1:n.493+861T>C

Variant summary

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

The ENST00000715996.1(ENSG00000258763):​n.493+861T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,172 control chromosomes in the GnomAD database, including 11,610 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 0.37 (11610 hom., cov: 33)
• Consequence: ENSG00000258763 ENST00000715996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440
• Publications: 3 publications found

Genes affected

ENSG00000258763 (HGNC:):

OR10P1 (HGNC:15378): (olfactory receptor family 10 subfamily P 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715996.1. 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
	OR10P1	NM_206899.1	MANE Select	c.*220A>G		downstream_gene	N/A	NP_996782.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258763	ENST00000715996.1		n.493+861T>C		intron	N/A
	OR10P1	ENST00000309675.3	TSL:6 MANE Select	c.*220A>G		downstream_gene	N/A	ENSP00000308082.2
	ENSG00000258763	ENST00000715997.1		n.*11T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57041 AN: 152054 Hom.: 11606 Cov.: 33

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.375 AC: 57056 AN: 152172 Hom.: 11610 Cov.: 33 AF XY: 0.370 AC XY: 27485 AN XY: 74384

African (AFR) AF: 0.249 AC: 10323 AN: 41522

American (AMR) AF: 0.393 AC: 6002 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1511 AN: 3472

East Asian (EAS) AF: 0.109 AC: 564 AN: 5176

South Asian (SAS) AF: 0.285 AC: 1373 AN: 4824

European-Finnish (FIN) AF: 0.407 AC: 4313 AN: 10598

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31605 AN: 67978

Other (OTH) AF: 0.394 AC: 830 AN: 2108

Alfa AF: 0.381 Hom.: 2690

Bravo AF: 0.369

Asia WGS AF: 0.215 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.3
DANN	Benign	0.68
PhyloP100		-0.44
Mutation Taster		=95/5	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs7309433; hg19: chr12-56031837;