Genetic Variant NM_001396058.1:c.324C>G (chr6-29553542-C-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001396058.1(OR2I1):c.324C>G(p.Ser108Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 398,340 control chromosomes in the GnomAD database, including 69,502 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 0.62 ( 29608 hom., cov: 36)

Exomes 𝑓: 0.57 ( 39894 hom. )

Consequence

OR2I1
NM_001396058.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -13.3

Publications

5 publications found

Variant links:

Genes affected

OR2I1 (HGNC:8258): (olfactory receptor family 2 subfamily I 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]

OR2I1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP7

Synonymous conserved (PhyloP=-13.3 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001396058.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2I1	NM_001396058.1	MANE Select	c.324C>G	p.Ser108Ser	synonymous	Exon 2 of 2	NP_001382987.1	Q8NGU4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
OR2I1	ENST00000641137.2	MANE Select	c.324C>G	p.Ser108Ser	synonymous	Exon 2 of 2	ENSP00000493715.1	Q8NGU4
OR2I1	ENST00000641730.1		n.1186C>G		non_coding_transcript_exon	Exon 2 of 2
OR2I1	ENST00000642037.1		n.512C>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.616

AC:

93737

AN:

152092

Hom.:

29560

Cov.:

show subpopulations

Gnomad AFR

AF:

0.742

Gnomad AMI

AF:

0.405

Gnomad AMR

AF:

0.585

Gnomad ASJ

AF:

0.489

Gnomad EAS

AF:

0.756

Gnomad SAS

AF:

0.785

Gnomad FIN

AF:

0.620

Gnomad MID

AF:

0.646

Gnomad NFE

AF:

0.533

Gnomad OTH

AF:

0.619

GnomAD4 exome

AF:

0.565

AC:

139064

AN:

246130

Hom.:

39894

Cov.:

AF XY:

0.561

AC XY:

70055

AN XY:

124792

show subpopulations

African (AFR)

AF:

0.742

AC:

5311

AN:

7160

American (AMR)

AF:

0.592

AC:

4395

AN:

7424

Ashkenazi Jewish (ASJ)

AF:

0.493

AC:

4547

AN:

9214

East Asian (EAS)

AF:

0.696

AC:

15940

AN:

22886

South Asian (SAS)

AF:

0.800

AC:

2427

AN:

3034

European-Finnish (FIN)

AF:

0.618

AC:

12884

AN:

20838

Middle Eastern (MID)

AF:

0.603

AC:

781

AN:

1296

European-Non Finnish (NFE)

AF:

0.527

AC:

83274

AN:

157926

Other (OTH)

AF:

0.581

AC:

9505

AN:

16352

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

4962

9925

14887

19850

24812

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

366

732

1098

1464

1830

<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:

0.617

AC:

93840

AN:

152210

Hom.:

29608

Cov.:

AF XY:

0.623

AC XY:

46345

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.742

AC:

30841

AN:

41546

American (AMR)

AF:

0.585

AC:

8960

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.489

AC:

1699

AN:

3472

East Asian (EAS)

AF:

0.756

AC:

3911

AN:

5172

South Asian (SAS)

AF:

0.783

AC:

3779

AN:

4828

European-Finnish (FIN)

AF:

0.620

AC:

6561

AN:

10588

Middle Eastern (MID)

AF:

0.656

AC:

193

AN:

294

European-Non Finnish (NFE)

AF:

0.533

AC:

36207

AN:

67980

Other (OTH)

AF:

0.624

AC:

1320

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1933

3866

5798

7731

9664

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

774

1548

2322

3096

3870

<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:

0.564

Hom.:

3062

Bravo

AF:

0.621

Asia WGS

AF:

0.786

AC:

2729

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.2

(source)

DANN

Benign

0.80

PhyloP100

-13

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over