Variant chr18-48029377-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_001318841.2(ZBTB7C):c.1743C>T(p.Asn581Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00201 in 1,555,300 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0015 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0021 ( 5 hom. )

Consequence

ZBTB7C
NM_001318841.2 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.218

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 18-48029377-G-A is Benign according to our data. Variant chr18-48029377-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 791653.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.218 with no splicing effect.

BS2

High AC in GnomAd4 at 235 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZBTB7C	NM_001318841.2 linkuse as main transcript	c.1743C>T	p.Asn581Asn	synonymous_variant	5/5	ENST00000590800.6	NP_001305770.1	A1YPR0B2RG49

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ZBTB7C	ENST00000590800.6 linkuse as main transcript	c.1743C>T	p.Asn581Asn	synonymous_variant	5/5	1	NM_001318841.2	ENSP00000467877.1	A1YPR0
ZBTB7C	ENST00000535628.6 linkuse as main transcript	c.1743C>T	p.Asn581Asn	synonymous_variant	3/3	1		ENSP00000439781.1	A1YPR0
ZBTB7C	ENST00000586438.5 linkuse as main transcript	c.1743C>T	p.Asn581Asn	synonymous_variant	3/3	1		ENSP00000468254.1	A1YPR0
ZBTB7C	ENST00000588982.5 linkuse as main transcript	c.1743C>T	p.Asn581Asn	synonymous_variant	4/4	1		ENSP00000468782.1	A1YPR0

Frequencies

GnomAD3 genomes

AF:

0.00155

AC:

235

AN:

152076

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000507

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00360

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0000943

Gnomad MID

AF:

0.00321

Gnomad NFE

AF:

0.00210

Gnomad OTH

AF:

0.00623

GnomAD3 exomes

AF:

0.00181

AC:

297

AN:

163758

Hom.:

AF XY:

0.00192

AC XY:

174

AN XY:

90842

show subpopulations

Gnomad AFR exome

AF:

0.000963

Gnomad AMR exome

AF:

0.00330

Gnomad ASJ exome

AF:

0.000821

Gnomad EAS exome

AF:

0.0000794

Gnomad SAS exome

AF:

0.0000407

Gnomad FIN exome

AF:

0.000108

Gnomad NFE exome

AF:

0.00258

Gnomad OTH exome

AF:

0.00239

GnomAD4 exome

AF:

0.00207

AC:

2898

AN:

1403112

Hom.:

Cov.:

AF XY:

0.00208

AC XY:

1447

AN XY:

694822

show subpopulations

Gnomad4 AFR exome

AF:

0.000664

Gnomad4 AMR exome

AF:

0.00362

Gnomad4 ASJ exome

AF:

0.000635

Gnomad4 EAS exome

AF:

0.0000550

Gnomad4 SAS exome

AF:

0.0000123

Gnomad4 FIN exome

AF:

0.000129

Gnomad4 NFE exome

AF:

0.00237

Gnomad4 OTH exome

AF:

0.00225

GnomAD4 genome

AF:

0.00154

AC:

235

AN:

152188

Hom.:

Cov.:

AF XY:

0.00140

AC XY:

104

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.000505

Gnomad4 AMR

AF:

0.00360

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0000943

Gnomad4 NFE

AF:

0.00210

Gnomad4 OTH

AF:

0.00617

Alfa

AF:

0.00142

Hom.:

Bravo

AF:

0.00194

Asia WGS

AF:

0.000579

AC:

AN:

3468

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Nov 01, 2022	ZBTB7C: BP4, BP7 -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	May 21, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

8.5

DANN

Benign

0.61

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