Genetic Variant OR6D1P:n.541C>T (chr10-45258725-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000436165.1(OR6D1P):n.541C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.459 in 152,186 control chromosomes in the GnomAD database, including 17,561 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 0.46 ( 17531 hom., cov: 32)

Exomes 𝑓: 0.62 ( 30 hom. )

Consequence

OR6D1P
ENST00000436165.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.56

Publications

1 publications found

Variant links:

Genes affected

OR6D1P (HGNC:14849): (olfactory receptor family 6 subfamily D member 1 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]

OR6D1P links:

ENSG00000293390 (HGNC:):

ENSG00000293390 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=-0.5).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR6D1P		n.45258725C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
OR6D1P	ENST00000436165.1 link	n.541C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000293390	ENST00000641007.1 link	n.763C>T	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000293390	ENST00000641209.1 link	n.333C>T	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.459

AC:

69787

AN:

151920

Hom.:

17526

Cov.:

show subpopulations

Gnomad AFR

AF:

0.260

Gnomad AMI

AF:

0.682

Gnomad AMR

AF:

0.455

Gnomad ASJ

AF:

0.476

Gnomad EAS

AF:

0.385

Gnomad SAS

AF:

0.402

Gnomad FIN

AF:

0.678

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.552

Gnomad OTH

AF:

0.476

GnomAD4 exome

AF:

0.623

AC:

AN:

146

Hom.:

Cov.:

AF XY:

0.568

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.694

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.628

AC:

AN:

Other (OTH)

AF:

0.900

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.528

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.459

AC:

69825

AN:

152040

Hom.:

17531

Cov.:

AF XY:

0.465

AC XY:

34596

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.260

AC:

10792

AN:

41458

American (AMR)

AF:

0.455

AC:

6949

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.476

AC:

1653

AN:

3472

East Asian (EAS)

AF:

0.386

AC:

1996

AN:

5172

South Asian (SAS)

AF:

0.402

AC:

1938

AN:

4816

European-Finnish (FIN)

AF:

0.678

AC:

7161

AN:

10566

Middle Eastern (MID)

AF:

0.548

AC:

160

AN:

292

European-Non Finnish (NFE)

AF:

0.552

AC:

37549

AN:

67966

Other (OTH)

AF:

0.477

AC:

1006

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1790

3580

5370

7160

8950

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

634

1268

1902

2536

3170

<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:

0.485

Hom.:

5773

Bravo

AF:

0.432

Asia WGS

AF:

0.413

AC:

1437

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

(source)

DANN

Benign

0.56

PhyloP100

5.6

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