dbSNP rs6456889: OR2W1-AS1:n.176+6829T>C (chr6-29043047-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000610326.2(OR2W1-AS1):n.176+6829T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,982 control chromosomes in the GnomAD database, including 10,267 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 0.34 ( 10267 hom., cov: 32)

Consequence

OR2W1-AS1
ENST00000610326.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.89

Publications

16 publications found

Variant links:

Genes affected

OR2W1-AS1 (HGNC:50896): (OR2W1 antisense RNA 1)

OR2W1-AS1 links:

Genome browser will be placed here

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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR2W1-AS1	NR_125387.1 link	n.30+6997T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
OR2W1-AS1	ENST00000610326.2 link	n.176+6829T>C	intron_variant	Intron 1 of 3	5
OR2W1-AS1	ENST00000623334.4 link	n.60+6997T>C	intron_variant	Intron 1 of 3	3
OR2W1-AS1	ENST00000623946.1 link	n.259-1198T>C	intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.338

AC:

51387

AN:

151864

Hom.:

10247

Cov.:

show subpopulations

Gnomad AFR

AF:

0.553

Gnomad AMI

AF:

0.128

Gnomad AMR

AF:

0.290

Gnomad ASJ

AF:

0.378

Gnomad EAS

AF:

0.227

Gnomad SAS

AF:

0.355

Gnomad FIN

AF:

0.286

Gnomad MID

AF:

0.261

Gnomad NFE

AF:

0.236

Gnomad OTH

AF:

0.339

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.339

AC:

51448

AN:

151982

Hom.:

10267

Cov.:

AF XY:

0.341

AC XY:

25301

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.553

AC:

22921

AN:

41452

American (AMR)

AF:

0.289

AC:

4416

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.378

AC:

1312

AN:

3470

East Asian (EAS)

AF:

0.226

AC:

1171

AN:

5180

South Asian (SAS)

AF:

0.355

AC:

1709

AN:

4820

European-Finnish (FIN)

AF:

0.286

AC:

3019

AN:

10550

Middle Eastern (MID)

AF:

0.250

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.236

AC:

16001

AN:

67934

Other (OTH)

AF:

0.336

AC:

709

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1628

3257

4885

6514

8142

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

494

988

1482

1976

2470

<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:

0.295

Hom.:

12738

Bravo

AF:

0.351

Asia WGS

AF:

0.286

AC:

998

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.5

(source)

DANN

Benign

0.40

PhyloP100

-1.9

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over