dbSNP rs6517137: OLIG2:c.*637T>C (chr21-33028471-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 NM_005806.4(OLIG2):c.*637T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 233,444 control chromosomes in the GnomAD database, including 1,585 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 0.11 ( 1135 hom., cov: 33)

Exomes 𝑓: 0.096 ( 450 hom. )

Consequence

OLIG2
NM_005806.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.837

Publications

8 publications found

Variant links:

Genes affected

OLIG2 (HGNC:9398): (oligodendrocyte transcription factor 2) This gene encodes a basic helix-loop-helix transcription factor which is expressed in oligodendroglial tumors of the brain. The protein is an essential regulator of ventral neuroectodermal progenitor cell fate. The gene is involved in a chromosomal translocation t(14;21)(q11.2;q22) associated with T-cell acute lymphoblastic leukemia. Its chromosomal location is within a region of chromosome 21 which has been suggested to play a role in learning deficits associated with Down syndrome. [provided by RefSeq, Jul 2008]

OLIG2 links:

ENSG00000227757 (HGNC:):

ENSG00000227757 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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OLIG2	NM_005806.4 link	c.*637T>C		3_prime_UTR_variant	Exon 2 of 2	ENST00000382357.4	NP_005797.1
OLIG2	XM_005260908.2 link	c.*637T>C		3_prime_UTR_variant	Exon 2 of 2		XP_005260965.1	Q13516

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OLIG2	ENST00000382357.4 link	c.*637T>C		3_prime_UTR_variant	Exon 2 of 2	1	NM_005806.4	ENSP00000371794.3		Q13516

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17102

AN:

152010

Hom.:

1127

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.151

Gnomad AMR

AF:

0.0955

Gnomad ASJ

AF:

0.0490

Gnomad EAS

AF:

0.0897

Gnomad SAS

AF:

0.172

Gnomad FIN

AF:

0.124

Gnomad MID

AF:

0.0573

Gnomad NFE

AF:

0.0772

Gnomad OTH

AF:

0.0990

GnomAD4 exome

AF:

0.0965

AC:

7846

AN:

81314

Hom.:

450

Cov.:

AF XY:

0.0971

AC XY:

3674

AN XY:

37838

show subpopulations

African (AFR)

AF:

0.189

AC:

576

AN:

3042

American (AMR)

AF:

0.0861

AC:

169

AN:

1962

Ashkenazi Jewish (ASJ)

AF:

0.0573

AC:

239

AN:

4172

East Asian (EAS)

AF:

0.0937

AC:

922

AN:

9836

South Asian (SAS)

AF:

0.183

AC:

107

AN:

586

European-Finnish (FIN)

AF:

0.133

AC:

1955

AN:

14744

Middle Eastern (MID)

AF:

0.0594

AC:

AN:

404

European-Non Finnish (NFE)

AF:

0.0810

AC:

3313

AN:

40924

Other (OTH)

AF:

0.0959

AC:

541

AN:

5644

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

372

743

1115

1486

1858

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.113

AC:

17127

AN:

152130

Hom.:

1135

Cov.:

AF XY:

0.116

AC XY:

8597

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.175

AC:

7271

AN:

41502

American (AMR)

AF:

0.0957

AC:

1464

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0490

AC:

170

AN:

3470

East Asian (EAS)

AF:

0.0891

AC:

460

AN:

5162

South Asian (SAS)

AF:

0.171

AC:

824

AN:

4810

European-Finnish (FIN)

AF:

0.124

AC:

1317

AN:

10600

Middle Eastern (MID)

AF:

0.0582

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0772

AC:

5249

AN:

67980

Other (OTH)

AF:

0.103

AC:

218

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

782

1564

2346

3128

3910

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

194

388

582

776

970

<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:

0.0893

Hom.:

2438

Bravo

AF:

0.110

Asia WGS

AF:

0.170

AC:

590

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.2

(source)

DANN

Benign

0.64

PhyloP100

-0.84

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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