Variant chr18-48029458-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001318841.2(ZBTB7C):c.1662A>G(p.Thr554=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 1,595,514 control chromosomes in the GnomAD database, including 77,881 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.36 ( 10693 hom., cov: 34)

Exomes 𝑓: 0.30 ( 67188 hom. )

Consequence

ZBTB7C
NM_001318841.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.05

Variant links:

Genes affected

ZBTB7C (HGNC:31700): (zinc finger and BTB domain containing 7C) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of cell population proliferation. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZBTB7C links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP6

Variant 18-48029458-T-C is Benign according to our data. Variant chr18-48029458-T-C is described in ClinVar as [Benign]. Clinvar id is 1270372.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.05 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB7C	NM_001318841.2 linkuse as main transcript	c.1662A>G	p.Thr554=	synonymous_variant	5/5	ENST00000590800.6	NP_001305770.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
ZBTB7C	ENST00000590800.6 linkuse as main transcript	c.1662A>G	p.Thr554=	synonymous_variant	5/5	1	NM_001318841.2	ENSP00000467877	P1
ZBTB7C	ENST00000535628.6 linkuse as main transcript	c.1662A>G	p.Thr554=	synonymous_variant	3/3	1		ENSP00000439781	P1
ZBTB7C	ENST00000586438.5 linkuse as main transcript	c.1662A>G	p.Thr554=	synonymous_variant	3/3	1		ENSP00000468254	P1
ZBTB7C	ENST00000588982.5 linkuse as main transcript	c.1662A>G	p.Thr554=	synonymous_variant	4/4	1		ENSP00000468782	P1

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

54760

AN:

151966

Hom.:

10666

Cov.:

show subpopulations

Gnomad AFR

AF:

0.502

Gnomad AMI

AF:

0.223

Gnomad AMR

AF:

0.378

Gnomad ASJ

AF:

0.284

Gnomad EAS

AF:

0.455

Gnomad SAS

AF:

0.337

Gnomad FIN

AF:

0.303

Gnomad MID

AF:

0.306

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.329

GnomAD3 exomes

AF:

0.333

AC:

74055

AN:

222526

Hom.:

13073

AF XY:

0.323

AC XY:

39728

AN XY:

123124

show subpopulations

Gnomad AFR exome

AF:

0.496

Gnomad AMR exome

AF:

0.434

Gnomad ASJ exome

AF:

0.286

Gnomad EAS exome

AF:

0.465

Gnomad SAS exome

AF:

0.331

Gnomad FIN exome

AF:

0.289

Gnomad NFE exome

AF:

0.270

Gnomad OTH exome

AF:

0.301

GnomAD4 exome

AF:

0.300

AC:

433023

AN:

1443438

Hom.:

67188

Cov.:

AF XY:

0.299

AC XY:

214882

AN XY:

718110

show subpopulations

Gnomad4 AFR exome

AF:

0.519

Gnomad4 AMR exome

AF:

0.429

Gnomad4 ASJ exome

AF:

0.292

Gnomad4 EAS exome

AF:

0.432

Gnomad4 SAS exome

AF:

0.333

Gnomad4 FIN exome

AF:

0.289

Gnomad4 NFE exome

AF:

0.281

Gnomad4 OTH exome

AF:

0.316

GnomAD4 genome

AF:

0.361

AC:

54835

AN:

152076

Hom.:

10693

Cov.:

AF XY:

0.362

AC XY:

26886

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.502

Gnomad4 AMR

AF:

0.378

Gnomad4 ASJ

AF:

0.284

Gnomad4 EAS

AF:

0.455

Gnomad4 SAS

AF:

0.336

Gnomad4 FIN

AF:

0.303

Gnomad4 NFE

AF:

0.280

Gnomad4 OTH

AF:

0.333

Alfa

AF:

0.296

Hom.:

2743

Bravo

AF:

0.377

Asia WGS

AF:

0.428

AC:

1464

AN:

3426

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 16, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

3.9

DANN

Benign

0.54

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