dbSNP rs12230513: OR6C64P:n.404A>G (chr12-55522996-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.53

Publications

7 publications found

Variant links:

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]

OR6C64P links:

ENSG00000258763 (HGNC:):

ENSG00000258763 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR6C64P		n.55522996A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
OR6C64P	ENST00000419708.1 link	n.404A>G	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000258763	ENST00000555138.2 link	n.143-29838T>C	intron_variant	Intron 2 of 3	2
ENSG00000258763	ENST00000556750.6 link	n.143-29838T>C	intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26387

AN:

152046

Hom.:

2615

Cov.:

show subpopulations

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.:

AF XY:

0.206

AC XY:

6834

AN XY:

33240

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.586

Heterozygous variant carriers

378

756

1135

1513

1891

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

160

320

480

640

800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.174

AC:

26402

AN:

152164

Hom.:

2623

Cov.:

AF XY:

0.174

AC XY:

12936

AN XY:

74376

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.190

AC:

12928

AN:

68002

Other (OTH)

AF:

0.202

AC:

428

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1087

2174

3262

4349

5436

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

294

588

882

1176

1470

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

1.4

(source)

DANN

Benign

0.82

PhyloP100

-1.5

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over