Variant 3-125232327-CT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_021964.3(ZNF148):c.*13del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.76 ( 42657 hom., cov: 0)

Exomes 𝑓: 0.49 ( 5175 hom. )

Failed GnomAD Quality Control

Consequence

ZNF148
NM_021964.3 3_prime_UTR

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: -0.285

Variant links:

Genes affected

ZNF148 (HGNC:12933): (zinc finger protein 148) The protein encoded by this gene is a member of the Kruppel family of zinc finger DNA binding proteins. The encoded protein activates transcription of the T-cell receptor and intestinal alkaline phosphatase genes but represses transcription of the ornithine decarboxylase, vimentin, gastrin, stomelysin, and enolase genes. Increased expression of this gene results in decreased patient survival rates from colorectal cancer, while mutations in this gene have been associated with global developmental delay, hypoplastic corpus callosum, and dysmorphic facies. [provided by RefSeq, Feb 2017]

ZNF148 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 3-125232327-CT-C is Benign according to our data. Variant chr3-125232327-CT-C is described in ClinVar as [Benign]. Clinvar id is 1179358.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF148	NM_021964.3 linkuse as main transcript	c.*13del		3_prime_UTR_variant	9/9	ENST00000360647.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF148	ENST00000360647.9 linkuse as main transcript	c.*13del		3_prime_UTR_variant	9/9	1	NM_021964.3	P1	Q9UQR1-1

Frequencies

GnomAD3 genomes

AF:

0.762

AC:

111650

AN:

146492

Hom.:

42656

Cov.:

show subpopulations

Gnomad AFR

AF:

0.846

Gnomad AMI

AF:

0.812

Gnomad AMR

AF:

0.686

Gnomad ASJ

AF:

0.812

Gnomad EAS

AF:

0.511

Gnomad SAS

AF:

0.661

Gnomad FIN

AF:

0.734

Gnomad MID

AF:

0.801

Gnomad NFE

AF:

0.755

Gnomad OTH

AF:

0.771

GnomAD3 exomes

AF:

0.478

AC:

72728

AN:

152218

Hom.:

965

AF XY:

0.477

AC XY:

39767

AN XY:

83400

show subpopulations

Gnomad AFR exome

AF:

0.494

Gnomad AMR exome

AF:

0.467

Gnomad ASJ exome

AF:

0.486

Gnomad EAS exome

AF:

0.468

Gnomad SAS exome

AF:

0.467

Gnomad FIN exome

AF:

0.484

Gnomad NFE exome

AF:

0.481

Gnomad OTH exome

AF:

0.481

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.486

AC:

630036

AN:

1295878

Hom.:

5175

Cov.:

AF XY:

0.485

AC XY:

310898

AN XY:

640700

show subpopulations

Gnomad4 AFR exome

AF:

0.495

Gnomad4 AMR exome

AF:

0.443

Gnomad4 ASJ exome

AF:

0.486

Gnomad4 EAS exome

AF:

0.463

Gnomad4 SAS exome

AF:

0.466

Gnomad4 FIN exome

AF:

0.477

Gnomad4 NFE exome

AF:

0.490

Gnomad4 OTH exome

AF:

0.486

GnomAD4 genome

AF:

0.762

AC:

111684

AN:

146568

Hom.:

42657

Cov.:

AF XY:

0.758

AC XY:

53938

AN XY:

71188

show subpopulations

Gnomad4 AFR

AF:

0.845

Gnomad4 AMR

AF:

0.686

Gnomad4 ASJ

AF:

0.812

Gnomad4 EAS

AF:

0.511

Gnomad4 SAS

AF:

0.659

Gnomad4 FIN

AF:

0.734

Gnomad4 NFE

AF:

0.755

Gnomad4 OTH

AF:

0.770

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 18, 2020

- -

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