Genetic Variant OLIG2:c.*1235T>G (chr21-33029069-T-G) – 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.*1235T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 237,012 control chromosomes in the GnomAD database, including 10,557 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 0.26 ( 6201 hom., cov: 34)

Exomes 𝑓: 0.30 ( 4356 hom. )

Consequence

OLIG2
NM_005806.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0920

Publications

5 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=-0.66).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OLIG2	NM_005806.4 link	c.*1235T>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000382357.4	NP_005797.1
OLIG2	XM_005260908.2 link	c.*1235T>G		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.*1235T>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_005806.4	ENSP00000371794.3		Q13516

Frequencies

GnomAD3 genomes

AF:

0.261

AC:

39742

AN:

152150

Hom.:

6203

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.125

Gnomad AMR

AF:

0.235

Gnomad ASJ

AF:

0.373

Gnomad EAS

AF:

0.0588

Gnomad SAS

AF:

0.304

Gnomad FIN

AF:

0.308

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.363

Gnomad OTH

AF:

0.298

GnomAD4 exome

AF:

0.302

AC:

25634

AN:

84744

Hom.:

4356

Cov.:

AF XY:

0.306

AC XY:

12010

AN XY:

39276

show subpopulations

African (AFR)

AF:

0.105

AC:

345

AN:

3280

American (AMR)

AF:

0.217

AC:

453

AN:

2088

Ashkenazi Jewish (ASJ)

AF:

0.384

AC:

1705

AN:

4442

East Asian (EAS)

AF:

0.0750

AC:

754

AN:

10050

South Asian (SAS)

AF:

0.290

AC:

183

AN:

630

European-Finnish (FIN)

AF:

0.293

AC:

4309

AN:

14726

Middle Eastern (MID)

AF:

0.346

AC:

150

AN:

434

European-Non Finnish (NFE)

AF:

0.368

AC:

15866

AN:

43172

Other (OTH)

AF:

0.316

AC:

1869

AN:

5922

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

851

1702

2554

3405

4256

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

108

144

180

<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:

0.261

AC:

39745

AN:

152268

Hom.:

6201

Cov.:

AF XY:

0.259

AC XY:

19284

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.103

AC:

4270

AN:

41544

American (AMR)

AF:

0.234

AC:

3583

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.373

AC:

1293

AN:

3470

East Asian (EAS)

AF:

0.0589

AC:

306

AN:

5192

South Asian (SAS)

AF:

0.305

AC:

1476

AN:

4832

European-Finnish (FIN)

AF:

0.308

AC:

3258

AN:

10584

Middle Eastern (MID)

AF:

0.320

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.364

AC:

24727

AN:

68024

Other (OTH)

AF:

0.295

AC:

624

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1510

3021

4531

6042

7552

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

422

844

1266

1688

2110

<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:

0.269

Hom.:

3201

Bravo

AF:

0.248

Asia WGS

AF:

0.144

AC:

500

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

(source)

DANN

Benign

0.75

PhyloP100

0.092

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