Genetic Variant TASOR:c.4483+26C>G (chr3-56624453-G-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_001365635.2(TASOR):c.4483+26C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 1,600,214 control chromosomes in the GnomAD database, including 65,753 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 0.32 ( 8076 hom., cov: 32)

Exomes 𝑓: 0.28 ( 57677 hom. )

Consequence

TASOR
NM_001365635.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.437

Publications

9 publications found

Variant links:

Genes affected

TASOR (HGNC:30314): (transcription activation suppressor) Enables chromatin binding activity. Involved in negative regulation of single stranded viral RNA replication via double stranded DNA intermediate; protein localization to heterochromatin; and regulation of gene expression. Located in heterochromatin and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TASOR 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=-0.53).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001365635.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TASOR	NM_001365635.2	MANE Select	c.4483+26C>G	intron	N/A	NP_001352564.1	Q9UK61-1
TASOR	NM_001365636.2		c.4360+26C>G	intron	N/A	NP_001352565.1
TASOR	NM_001363940.1		c.4300+26C>G	intron	N/A	NP_001350869.1	Q9UK61-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TASOR	ENST00000683822.1	MANE Select	c.4483+26C>G	intron	N/A	ENSP00000508241.1	Q9UK61-1
TASOR	ENST00000355628.9	TSL:1	c.4300+26C>G	intron	N/A	ENSP00000347845.5	Q9UK61-4
TASOR	ENST00000431842.6	TSL:1	c.3172+26C>G	intron	N/A	ENSP00000399410.2	Q9UK61-2

Frequencies

GnomAD3 genomes

AF:

0.317

AC:

48169

AN:

151832

Hom.:

8072

Cov.:

show subpopulations

Gnomad AFR

AF:

0.373

Gnomad AMI

AF:

0.344

Gnomad AMR

AF:

0.435

Gnomad ASJ

AF:

0.212

Gnomad EAS

AF:

0.485

Gnomad SAS

AF:

0.239

Gnomad FIN

AF:

0.311

Gnomad MID

AF:

0.163

Gnomad NFE

AF:

0.257

Gnomad OTH

AF:

0.314

GnomAD2 exomes

AF:

0.316

AC:

76569

AN:

241960

AF XY:

0.303

show subpopulations

Gnomad AFR exome

AF:

0.374

Gnomad AMR exome

AF:

0.506

Gnomad ASJ exome

AF:

0.233

Gnomad EAS exome

AF:

0.480

Gnomad FIN exome

AF:

0.305

Gnomad NFE exome

AF:

0.258

Gnomad OTH exome

AF:

0.282

GnomAD4 exome

AF:

0.276

AC:

399088

AN:

1448264

Hom.:

57677

Cov.:

AF XY:

0.273

AC XY:

196208

AN XY:

720022

show subpopulations

African (AFR)

AF:

0.365

AC:

11917

AN:

32666

American (AMR)

AF:

0.495

AC:

20694

AN:

41774

Ashkenazi Jewish (ASJ)

AF:

0.228

AC:

5851

AN:

25636

East Asian (EAS)

AF:

0.465

AC:

18379

AN:

39556

South Asian (SAS)

AF:

0.237

AC:

20033

AN:

84510

European-Finnish (FIN)

AF:

0.298

AC:

15853

AN:

53154

Middle Eastern (MID)

AF:

0.156

AC:

887

AN:

5674

European-Non Finnish (NFE)

AF:

0.261

AC:

288385

AN:

1105446

Other (OTH)

AF:

0.286

AC:

17089

AN:

59848

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

12809

25618

38426

51235

64044

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10052

20104

30156

40208

50260

<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:

0.317

AC:

48209

AN:

151950

Hom.:

8076

Cov.:

AF XY:

0.321

AC XY:

23868

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.372

AC:

15412

AN:

41438

American (AMR)

AF:

0.436

AC:

6660

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.212

AC:

736

AN:

3470

East Asian (EAS)

AF:

0.485

AC:

2502

AN:

5154

South Asian (SAS)

AF:

0.239

AC:

1153

AN:

4824

European-Finnish (FIN)

AF:

0.311

AC:

3278

AN:

10528

Middle Eastern (MID)

AF:

0.176

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.257

AC:

17440

AN:

67948

Other (OTH)

AF:

0.314

AC:

663

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1620

3240

4859

6479

8099

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

470

940

1410

1880

2350

<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:

0.197

Hom.:

613

Bravo

AF:

0.332

Asia WGS

AF:

0.361

AC:

1257

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

(source)

DANN

Benign

0.68

PhyloP100

0.44

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

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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