chr12-55522996-A-G

Variant names:

• chr12-55522996-A-G
• rs12230513
• ENST00000419708.1:n.404A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419708.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR6C64P	ENST00000419708.1	TSL:6	n.404A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000258763	ENST00000555138.2	TSL:2	n.143-29838T>C		intron	N/A
	ENSG00000258763	ENST00000556750.6	TSL:2	n.143-29838T>C		intron	N/A

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

African (AFR) AF: 0.0871 AC: 159 AN: 1826

American (AMR) AF: 0.256 AC: 1991 AN: 7774

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 159 AN: 788

East Asian (EAS) AF: 0.405 AC: 1513 AN: 3738

South Asian (SAS) AF: 0.157 AC: 898 AN: 5732

European-Finnish (FIN) AF: 0.199 AC: 1027 AN: 5158

Middle Eastern (MID) AF: 0.371 AC: 130 AN: 350

European-Non Finnish (NFE) AF: 0.203 AC: 5917 AN: 29094

Other (OTH) AF: 0.200 AC: 429 AN: 2146

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

African (AFR) AF: 0.0989 AC: 4107 AN: 41526

American (AMR) AF: 0.213 AC: 3257 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 636 AN: 3466

East Asian (EAS) AF: 0.424 AC: 2190 AN: 5164

South Asian (SAS) AF: 0.135 AC: 649 AN: 4824

European-Finnish (FIN) AF: 0.187 AC: 1978 AN: 10578

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12928 AN: 68002

Other (OTH) AF: 0.202 AC: 428 AN: 2116

Alfa AF: 0.182 Hom.: 6563

Bravo AF: 0.176

Asia WGS AF: 0.240 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	1.4
DANN	Benign	0.82
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12230513; hg19: chr12-55916780;