Genetic Variant TUT7:c.3029-39C>A (chr9-86319709-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_024617.4(TUT7):c.3029-39C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 1,338,518 control chromosomes in the GnomAD database, including 224,378 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 0.63 ( 30897 hom., cov: 33)

Exomes 𝑓: 0.57 ( 193481 hom. )

Consequence

TUT7
NM_024617.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.515

Publications

9 publications found

Variant links:

Genes affected

TUT7 (HGNC:25817): (terminal uridylyl transferase 7) Enables RNA uridylyltransferase activity and miRNA binding activity. Involved in RNA metabolic process and negative regulation of transposition, RNA-mediated. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TUT7 links:

ENSG00000299358 (HGNC:):

ENSG00000299358 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024617.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TUT7	NM_024617.4	MANE Select	c.3029-39C>A	intron	N/A	NP_078893.2
TUT7	NM_001185059.2		c.3029-39C>A	intron	N/A	NP_001171988.1	Q5VYS8-1
TUT7	NM_001185074.2		c.2509-2433C>A	intron	N/A	NP_001172003.1	Q5VYS8-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TUT7	ENST00000375963.8	TSL:5 MANE Select	c.3029-39C>A	intron	N/A	ENSP00000365130.3	Q5VYS8-1
TUT7	ENST00000375960.6	TSL:1	c.2509-2433C>A	intron	N/A	ENSP00000365127.2	Q5VYS8-4
TUT7	ENST00000896499.1		c.3029-39C>A	intron	N/A	ENSP00000566558.1

Frequencies

GnomAD3 genomes

AF:

0.627

AC:

95324

AN:

151942

Hom.:

30858

Cov.:

show subpopulations

Gnomad AFR

AF:

0.792

Gnomad AMI

AF:

0.549

Gnomad AMR

AF:

0.563

Gnomad ASJ

AF:

0.444

Gnomad EAS

AF:

0.551

Gnomad SAS

AF:

0.566

Gnomad FIN

AF:

0.642

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.562

Gnomad OTH

AF:

0.564

GnomAD2 exomes

AF:

0.576

AC:

107478

AN:

186746

AF XY:

0.569

show subpopulations

Gnomad AFR exome

AF:

0.801

Gnomad AMR exome

AF:

0.556

Gnomad ASJ exome

AF:

0.458

Gnomad EAS exome

AF:

0.541

Gnomad FIN exome

AF:

0.640

Gnomad NFE exome

AF:

0.557

Gnomad OTH exome

AF:

0.546

GnomAD4 exome

AF:

0.569

AC:

674932

AN:

1186458

Hom.:

193481

Cov.:

AF XY:

0.567

AC XY:

340275

AN XY:

600126

show subpopulations

African (AFR)

AF:

0.801

AC:

20640

AN:

25766

American (AMR)

AF:

0.551

AC:

16756

AN:

30432

Ashkenazi Jewish (ASJ)

AF:

0.456

AC:

10455

AN:

22950

East Asian (EAS)

AF:

0.625

AC:

23168

AN:

37042

South Asian (SAS)

AF:

0.559

AC:

39420

AN:

70558

European-Finnish (FIN)

AF:

0.639

AC:

31931

AN:

49940

Middle Eastern (MID)

AF:

0.494

AC:

2376

AN:

4808

European-Non Finnish (NFE)

AF:

0.561

AC:

501483

AN:

894378

Other (OTH)

AF:

0.567

AC:

28703

AN:

50584

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

13423

26846

40269

53692

67115

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13124

26248

39372

52496

65620

<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:

0.627

AC:

95414

AN:

152060

Hom.:

30897

Cov.:

AF XY:

0.630

AC XY:

46818

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.792

AC:

32881

AN:

41494

American (AMR)

AF:

0.563

AC:

8601

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.444

AC:

1538

AN:

3464

East Asian (EAS)

AF:

0.550

AC:

2847

AN:

5178

South Asian (SAS)

AF:

0.568

AC:

2740

AN:

4828

European-Finnish (FIN)

AF:

0.642

AC:

6770

AN:

10540

Middle Eastern (MID)

AF:

0.414

AC:

121

AN:

292

European-Non Finnish (NFE)

AF:

0.563

AC:

38231

AN:

67964

Other (OTH)

AF:

0.562

AC:

1185

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1746

3493

5239

6986

8732

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

770

1540

2310

3080

3850

<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:

0.509

Hom.:

2797

Bravo

AF:

0.626

Asia WGS

AF:

0.564

AC:

1961

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.62

(source)

DANN

Benign

0.44

PhyloP100

0.52

PromoterAI

-0.0016

Neutral

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over