dbSNP rs3753603: ZBTB8OS:c.*26C>T (chr1-32621836-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_178547.5(ZBTB8OS):c.*26C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0582 in 1,484,284 control chromosomes in the GnomAD database, including 6,564 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 0.14 ( 2900 hom., cov: 32)

Exomes 𝑓: 0.049 ( 3664 hom. )

Consequence

ZBTB8OS
NM_178547.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.120

Publications

9 publications found

Variant links:

Genes affected

ZBTB8OS (HGNC:24094): (zinc finger and BTB domain containing 8 opposite strand) Predicted to enable metal ion binding activity. Involved in tRNA splicing, via endonucleolytic cleavage and ligation. Part of tRNA-splicing ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

ZBTB8OS 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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZBTB8OS	NM_178547.5 link	c.*26C>T		3_prime_UTR_variant	Exon 7 of 7	ENST00000468695.6	NP_848642.2	Q8IWT0-1A8K0B5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZBTB8OS	ENST00000468695.6 link	c.*26C>T		3_prime_UTR_variant	Exon 7 of 7	1	NM_178547.5	ENSP00000417677.2		Q8IWT0-1A8K0B5

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20674

AN:

151822

Hom.:

2896

Cov.:

show subpopulations

Gnomad AFR

AF:

0.349

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.150

Gnomad ASJ

AF:

0.0383

Gnomad EAS

AF:

0.115

Gnomad SAS

AF:

0.0596

Gnomad FIN

AF:

0.0217

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0361

Gnomad OTH

AF:

0.133

GnomAD2 exomes

AF:

0.0759

AC:

16587

AN:

218412

AF XY:

0.0673

show subpopulations

Gnomad AFR exome

AF:

0.351

Gnomad AMR exome

AF:

0.139

Gnomad ASJ exome

AF:

0.0362

Gnomad EAS exome

AF:

0.119

Gnomad FIN exome

AF:

0.0209

Gnomad NFE exome

AF:

0.0357

Gnomad OTH exome

AF:

0.0595

GnomAD4 exome

AF:

0.0493

AC:

65672

AN:

1332344

Hom.:

3664

Cov.:

AF XY:

0.0484

AC XY:

32337

AN XY:

667962

show subpopulations

African (AFR)

AF:

0.362

AC:

10526

AN:

29078

American (AMR)

AF:

0.146

AC:

4702

AN:

32164

Ashkenazi Jewish (ASJ)

AF:

0.0391

AC:

960

AN:

24522

East Asian (EAS)

AF:

0.115

AC:

4417

AN:

38360

South Asian (SAS)

AF:

0.0546

AC:

4162

AN:

76292

European-Finnish (FIN)

AF:

0.0212

AC:

1114

AN:

52594

Middle Eastern (MID)

AF:

0.0675

AC:

263

AN:

3894

European-Non Finnish (NFE)

AF:

0.0350

AC:

35686

AN:

1019692

Other (OTH)

AF:

0.0689

AC:

3842

AN:

55748

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

2720

5439

8159

10878

13598

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.136

AC:

20716

AN:

151940

Hom.:

2900

Cov.:

AF XY:

0.135

AC XY:

10043

AN XY:

74252

show subpopulations

African (AFR)

AF:

0.348

AC:

14410

AN:

41380

American (AMR)

AF:

0.150

AC:

2291

AN:

15234

Ashkenazi Jewish (ASJ)

AF:

0.0383

AC:

133

AN:

3470

East Asian (EAS)

AF:

0.115

AC:

598

AN:

5178

South Asian (SAS)

AF:

0.0594

AC:

286

AN:

4814

European-Finnish (FIN)

AF:

0.0217

AC:

229

AN:

10566

Middle Eastern (MID)

AF:

0.0884

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0361

AC:

2452

AN:

67984

Other (OTH)

AF:

0.132

AC:

279

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

757

1514

2271

3028

3785

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0837

Hom.:

371

Bravo

AF:

0.159

Asia WGS

AF:

0.0960

AC:

334

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.0

(source)

DANN

Benign

0.61

PhyloP100

-0.12

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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rs3753603

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