Genetic Variant ENST00000616197.2:n.709A>T (chr11-130403335-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000616197.2(ZBTB44-DT):n.709A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 153,428 control chromosomes in the GnomAD database, including 7,233 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 0.29 ( 7159 hom., cov: 33)

Exomes 𝑓: 0.31 ( 74 hom. )

Consequence

ZBTB44-DT
ENST00000616197.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.354

Publications

40 publications found

Variant links:

Genes affected

ZBTB44-DT (HGNC:54265): (ZBTB44 divergent transcript)

ZBTB44-DT links:

ENSG00000301332 (HGNC:):

ENSG00000301332 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=-0.52).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZBTB44-DT	NR_148980.1 link	n.646A>T		non_coding_transcript_exon_variant	Exon 7 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ZBTB44-DT	ENST00000616197.2 link	n.709A>T	non_coding_transcript_exon_variant	Exon 7 of 7	3
ZBTB44-DT	ENST00000649867.1 link	n.502A>T	non_coding_transcript_exon_variant	Exon 6 of 6
ZBTB44-DT	ENST00000777860.1 link	n.377A>T	non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.295

AC:

44856

AN:

152034

Hom.:

7157

Cov.:

show subpopulations

Gnomad AFR

AF:

0.226

Gnomad AMI

AF:

0.468

Gnomad AMR

AF:

0.297

Gnomad ASJ

AF:

0.273

Gnomad EAS

AF:

0.0306

Gnomad SAS

AF:

0.257

Gnomad FIN

AF:

0.338

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.352

Gnomad OTH

AF:

0.289

GnomAD4 exome

AF:

0.306

AC:

391

AN:

1276

Hom.:

Cov.:

AF XY:

0.315

AC XY:

213

AN XY:

676

show subpopulations

African (AFR)

AF:

0.318

AC:

AN:

American (AMR)

AF:

0.233

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.292

AC:

AN:

East Asian (EAS)

AF:

0.0507

AC:

AN:

138

South Asian (SAS)

AF:

0.167

AC:

AN:

European-Finnish (FIN)

AF:

0.307

AC:

AN:

192

Middle Eastern (MID)

AF:

0.167

AC:

AN:

European-Non Finnish (NFE)

AF:

0.362

AC:

283

AN:

782

Other (OTH)

AF:

0.257

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.295

AC:

44872

AN:

152152

Hom.:

7159

Cov.:

AF XY:

0.293

AC XY:

21756

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.226

AC:

9375

AN:

41512

American (AMR)

AF:

0.297

AC:

4546

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.273

AC:

947

AN:

3470

East Asian (EAS)

AF:

0.0311

AC:

161

AN:

5182

South Asian (SAS)

AF:

0.256

AC:

1236

AN:

4824

European-Finnish (FIN)

AF:

0.338

AC:

3569

AN:

10560

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.352

AC:

23940

AN:

67994

Other (OTH)

AF:

0.292

AC:

616

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1612

3224

4837

6449

8061

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

440

880

1320

1760

2200

<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:

0.330

Hom.:

4797

Bravo

AF:

0.287

Asia WGS

AF:

0.149

AC:

520

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

(source)

DANN

Benign

0.85

PhyloP100

0.35

Splicing

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