dbSNP rs10510787: TASOR:p.Gln1607Gln (chr3-56623229-C-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_001365635.2(TASOR):c.4821G>A(p.Gln1607Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0159 in 1,613,328 control chromosomes in the GnomAD database, including 318 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 0.027 ( 97 hom., cov: 32)

Exomes 𝑓: 0.015 ( 221 hom. )

Consequence

TASOR
NM_001365635.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.361

Publications

3 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.29).

BP7

Synonymous conserved (PhyloP=0.361 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TASOR	NM_001365635.2 link	c.4821G>A	p.Gln1607Gln	synonymous_variant	Exon 24 of 24	ENST00000683822.1	NP_001352564.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TASOR	ENST00000683822.1 link	c.4821G>A	p.Gln1607Gln	synonymous_variant	Exon 24 of 24		NM_001365635.2	ENSP00000508241.1		Q9UK61-1

Frequencies

GnomAD3 genomes

AF:

0.0266

AC:

4047

AN:

152110

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0618

Gnomad AMI

AF:

0.0330

Gnomad AMR

AF:

0.0132

Gnomad ASJ

AF:

0.0161

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0157

Gnomad FIN

AF:

0.00462

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0149

Gnomad OTH

AF:

0.0259

GnomAD2 exomes

AF:

0.0155

AC:

3891

AN:

250750

AF XY:

0.0156

show subpopulations

Gnomad AFR exome

AF:

0.0601

Gnomad AMR exome

AF:

0.00985

Gnomad ASJ exome

AF:

0.0152

Gnomad EAS exome

AF:

0.000109

Gnomad FIN exome

AF:

0.00464

Gnomad NFE exome

AF:

0.0156

Gnomad OTH exome

AF:

0.0167

GnomAD4 exome

AF:

0.0148

AC:

21596

AN:

1461100

Hom.:

221

Cov.:

AF XY:

0.0149

AC XY:

10812

AN XY:

726850

show subpopulations

African (AFR)

AF:

0.0630

AC:

2107

AN:

33450

American (AMR)

AF:

0.0109

AC:

487

AN:

44714

Ashkenazi Jewish (ASJ)

AF:

0.0154

AC:

401

AN:

26122

East Asian (EAS)

AF:

0.00

AC:

AN:

39638

South Asian (SAS)

AF:

0.0157

AC:

1349

AN:

86194

European-Finnish (FIN)

AF:

0.00538

AC:

287

AN:

53306

Middle Eastern (MID)

AF:

0.0312

AC:

173

AN:

5540

European-Non Finnish (NFE)

AF:

0.0142

AC:

15763

AN:

1111786

Other (OTH)

AF:

0.0171

AC:

1029

AN:

60350

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

1092

2184

3276

4368

5460

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

612

1224

1836

2448

3060

<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:

0.0268

AC:

4074

AN:

152228

Hom.:

Cov.:

AF XY:

0.0261

AC XY:

1945

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.0622

AC:

2583

AN:

41540

American (AMR)

AF:

0.0132

AC:

202

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0161

AC:

AN:

3468

East Asian (EAS)

AF:

0.000193

AC:

AN:

5182

South Asian (SAS)

AF:

0.0156

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00462

AC:

AN:

10600

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0149

AC:

1013

AN:

68012

Other (OTH)

AF:

0.0280

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

189

377

566

754

943

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

192

240

<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:

0.0200

Hom.:

132

Bravo

AF:

0.0284

Asia WGS

AF:

0.0180

AC:

AN:

3478

EpiCase

AF:

0.0190

EpiControl

AF:

0.0190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.29

CADD

Benign

4.0

(source)

DANN

Benign

0.76

PhyloP100

0.36

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over