Genetic Variant NM_024617.4:c.1455+21T>G (chr9-86337398-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_024617.4(TUT7):c.1455+21T>G variant causes a intron change. The variant allele was found at a frequency of 0.0315 in 1,596,050 control chromosomes in the GnomAD database, including 955 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 0.024 ( 73 hom., cov: 32)

Exomes 𝑓: 0.032 ( 882 hom. )

Consequence

TUT7
NM_024617.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.89

Publications

3 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:

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=-0.79).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0244 (3722/152304) while in subpopulation NFE AF = 0.0381 (2594/68026). AF 95% confidence interval is 0.0369. There are 73 homozygotes in GnomAd4. There are 1786 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 73 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TUT7	NM_024617.4 link	c.1455+21T>G		intron_variant	Intron 10 of 26	ENST00000375963.8	NP_078893.2	Q5VYS8-1Q96KX5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TUT7	ENST00000375963.8 link	c.1455+21T>G		intron_variant	Intron 10 of 26	5	NM_024617.4	ENSP00000365130.3		Q5VYS8-1

Frequencies

GnomAD3 genomes

AF:

0.0245

AC:

3722

AN:

152186

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00567

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.0276

Gnomad ASJ

AF:

0.0395

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00766

Gnomad FIN

AF:

0.0216

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0381

Gnomad OTH

AF:

0.0229

GnomAD2 exomes

AF:

0.0255

AC:

5863

AN:

230060

AF XY:

0.0260

show subpopulations

Gnomad AFR exome

AF:

0.00588

Gnomad AMR exome

AF:

0.0179

Gnomad ASJ exome

AF:

0.0410

Gnomad EAS exome

AF:

0.000118

Gnomad FIN exome

AF:

0.0220

Gnomad NFE exome

AF:

0.0373

Gnomad OTH exome

AF:

0.0291

GnomAD4 exome

AF:

0.0322

AC:

46482

AN:

1443746

Hom.:

882

Cov.:

AF XY:

0.0317

AC XY:

22772

AN XY:

718092

show subpopulations

African (AFR)

AF:

0.00467

AC:

150

AN:

32132

American (AMR)

AF:

0.0177

AC:

687

AN:

38824

Ashkenazi Jewish (ASJ)

AF:

0.0370

AC:

926

AN:

25036

East Asian (EAS)

AF:

0.000101

AC:

AN:

39576

South Asian (SAS)

AF:

0.0109

AC:

898

AN:

82620

European-Finnish (FIN)

AF:

0.0216

AC:

1148

AN:

53174

Middle Eastern (MID)

AF:

0.00529

AC:

AN:

5666

European-Non Finnish (NFE)

AF:

0.0371

AC:

41073

AN:

1107122

Other (OTH)

AF:

0.0263

AC:

1566

AN:

59596

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

2005

4009

6014

8018

10023

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1478

2956

4434

5912

7390

<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:

0.0244

AC:

3722

AN:

152304

Hom.:

Cov.:

AF XY:

0.0240

AC XY:

1786

AN XY:

74480

show subpopulations

African (AFR)

AF:

0.00565

AC:

235

AN:

41560

American (AMR)

AF:

0.0276

AC:

422

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0395

AC:

137

AN:

3470

East Asian (EAS)

AF:

0.000193

AC:

AN:

5190

South Asian (SAS)

AF:

0.00766

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.0216

AC:

229

AN:

10620

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0381

AC:

2594

AN:

68026

Other (OTH)

AF:

0.0227

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

192

385

577

770

962

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

160

200

<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:

0.0336

Hom.:

291

Bravo

AF:

0.0231

Asia WGS

AF:

0.00664

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

(source)

DANN

Benign

0.77

PhyloP100

5.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

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