Variant chr8-80486812-TGTC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PM4_SupportingBP6_ModerateBA1

The NM_001105539.3(ZBTB10):c.5_7delCGT(p.Ser2del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0405 in 1,446,172 control chromosomes in the GnomAD database, including 1,665 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.036 ( 205 hom., cov: 31)

Exomes 𝑓: 0.041 ( 1460 hom. )

Consequence

ZBTB10
NM_001105539.3 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.23

Variant links:

Genes affected

ZBTB10 (HGNC:30953): (zinc finger and BTB domain containing 10) Predicted to enable RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZBTB10 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_001105539.3. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant 8-80486812-TGTC-T is Benign according to our data. Variant chr8-80486812-TGTC-T is described in ClinVar as [Benign]. Clinvar id is 1245018.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB10	NM_001105539.3 linkuse as main transcript	c.5_7delCGT	p.Ser2del	disruptive_inframe_deletion	1/6	ENST00000455036.8	NP_001099009.1	Q96DT7-1
ZBTB10	NM_023929.5 linkuse as main transcript	c.5_7delCGT	p.Ser2del	disruptive_inframe_deletion	1/7		NP_076418.3	Q96DT7-2Q9H9H3
ZBTB10	NM_001277145.2 linkuse as main transcript	c.96+936_96+938delCGT		intron_variant			NP_001264074.1	Q96DT7-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ZBTB10	ENST00000455036.8 linkuse as main transcript	c.5_7delCGT	p.Ser2del	disruptive_inframe_deletion	1/6	2	NM_001105539.3	ENSP00000412036.3	Q96DT7-1
ZBTB10	ENST00000430430.5 linkuse as main transcript	c.5_7delCGT	p.Ser2del	disruptive_inframe_deletion	2/7	5		ENSP00000387462.1	Q96DT7-1
ZBTB10	ENST00000426744.5 linkuse as main transcript	c.5_7delCGT	p.Ser2del	disruptive_inframe_deletion	1/7	5		ENSP00000416134.2	Q96DT7-2
ZBTB10	ENST00000379091.8 linkuse as main transcript	c.96+936_96+938delCGT		intron_variant		2		ENSP00000368384.4	Q96DT7-4

Frequencies

GnomAD3 genomes

AF:

0.0357

AC:

5326

AN:

149304

Hom.:

203

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00685

Gnomad AMI

AF:

0.00223

Gnomad AMR

AF:

0.0234

Gnomad ASJ

AF:

0.0174

Gnomad EAS

AF:

0.213

Gnomad SAS

AF:

0.0746

Gnomad FIN

AF:

0.0515

Gnomad MID

AF:

0.0327

Gnomad NFE

AF:

0.0389

Gnomad OTH

AF:

0.0372

GnomAD3 exomes

AF:

0.0421

AC:

2741

AN:

65104

Hom.:

113

AF XY:

0.0432

AC XY:

1630

AN XY:

37746

show subpopulations

Gnomad AFR exome

AF:

0.00563

Gnomad AMR exome

AF:

0.0138

Gnomad ASJ exome

AF:

0.0147

Gnomad EAS exome

AF:

0.201

Gnomad SAS exome

AF:

0.0644

Gnomad FIN exome

AF:

0.0472

Gnomad NFE exome

AF:

0.0357

Gnomad OTH exome

AF:

0.0313

GnomAD4 exome

AF:

0.0411

AC:

53240

AN:

1296754

Hom.:

1460

AF XY:

0.0415

AC XY:

26489

AN XY:

638174

show subpopulations

Gnomad4 AFR exome

AF:

0.00716

Gnomad4 AMR exome

AF:

0.0202

Gnomad4 ASJ exome

AF:

0.0158

Gnomad4 EAS exome

AF:

0.158

Gnomad4 SAS exome

AF:

0.0704

Gnomad4 FIN exome

AF:

0.0506

Gnomad4 NFE exome

AF:

0.0370

Gnomad4 OTH exome

AF:

0.0470

GnomAD4 genome

AF:

0.0356

AC:

5324

AN:

149418

Hom.:

205

Cov.:

AF XY:

0.0376

AC XY:

2743

AN XY:

72960

show subpopulations

Gnomad4 AFR

AF:

0.00683

Gnomad4 AMR

AF:

0.0234

Gnomad4 ASJ

AF:

0.0174

Gnomad4 EAS

AF:

0.214

Gnomad4 SAS

AF:

0.0747

Gnomad4 FIN

AF:

0.0515

Gnomad4 NFE

AF:

0.0389

Gnomad4 OTH

AF:

0.0367

Alfa

AF:

0.0373

Hom.:

Bravo

AF:

0.0327

Asia WGS

AF:

0.122

AC:

417

AN:

3428

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over