rs12230513

Positions:

• chr12-55522996-A-G

Variant summary

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

The ENST00000419708.1(OR6C64P):​n.404A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 208,770 control chromosomes in the GnomAD database, including 4,008 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 0.17 (2623 hom., cov: 32)
  • Exomes 𝑓: 0.22 (1385 hom.)
• Consequence: OR6C64P ENST00000419708.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

OR6C64P (HGNC:31294): (olfactory receptor family 6 subfamily C member 64 pseudogene) 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]

ENSG00000258763 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR6C64P		n.55522996A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR6C64P	ENST00000419708.1	n.404A>G		non_coding_transcript_exon_variant	1/1	6
ENSG00000258763	ENST00000555138.1	n.58-29838T>C		intron_variant		2
ENSG00000258763	ENST00000556750.5	n.58-29838T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26387 AN: 152046 Hom.: 2615 Cov.: 32

Gnomad AFR AF: 0.0990

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.197

GnomAD4 exome AF: 0.216 AC: 12223 AN: 56606 Hom.: 1385 Cov.: 0 AF XY: 0.206 AC XY: 6834 AN XY: 33240

Gnomad4 AFR exome AF: 0.0871

Gnomad4 AMR exome AF: 0.256

Gnomad4 ASJ exome AF: 0.202

Gnomad4 EAS exome AF: 0.405

Gnomad4 SAS exome AF: 0.157

Gnomad4 FIN exome AF: 0.199

Gnomad4 NFE exome AF: 0.203

Gnomad4 OTH exome AF: 0.200

GnomAD4 genome AF: 0.174 AC: 26402 AN: 152164 Hom.: 2623 Cov.: 32 AF XY: 0.174 AC XY: 12936 AN XY: 74376

Gnomad4 AFR AF: 0.0989

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.202

Alfa AF: 0.187 Hom.: 4325

Bravo AF: 0.176

Asia WGS AF: 0.240 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	1.4
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12230513; hg19: chr12-55916780;