Genetic Variant ZNF341:c.31+36C>T (chr20-33732088-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001282933.2(ZNF341):c.31+36C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 1,222,268 control chromosomes in the GnomAD database, including 23,121 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.15 ( 2339 hom., cov: 31)

Exomes 𝑓: 0.18 ( 20782 hom. )

Consequence

ZNF341
NM_001282933.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.88

Variant links:

Genes affected

ZNF341 (HGNC:15992): (zinc finger protein 341) Enables DNA binding activity and DNA-binding transcription activator activity. Predicted to be involved in regulation of transcription, DNA-templated. Located in nucleus. Implicated in hyper IgE recurrent infection syndrome 3. [provided by Alliance of Genome Resources, Apr 2022]

ZNF341 links:

LOC124904890 (HGNC:):

LOC124904890 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 20-33732088-C-T is Benign according to our data. Variant chr20-33732088-C-T is described in ClinVar as [Benign]. Clinvar id is 2688478.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF341	NM_001282933.2 link	c.31+36C>T		intron_variant	Intron 1 of 14	ENST00000375200.6	NP_001269862.1	Q9BYN7-1Q504V9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF341	ENST00000375200.6 link	c.31+36C>T		intron_variant	Intron 1 of 14	1	NM_001282933.2	ENSP00000364346.1		Q9BYN7-1

Frequencies

GnomAD3 genomes

AF:

0.146

AC:

21792

AN:

149772

Hom.:

2337

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0331

Gnomad AMI

AF:

0.222

Gnomad AMR

AF:

0.134

Gnomad ASJ

AF:

0.200

Gnomad EAS

AF:

0.526

Gnomad SAS

AF:

0.288

Gnomad FIN

AF:

0.155

Gnomad MID

AF:

0.223

Gnomad NFE

AF:

0.172

Gnomad OTH

AF:

0.158

GnomAD3 exomes

AF:

0.195

AC:

633

AN:

3238

Hom.:

AF XY:

0.203

AC XY:

349

AN XY:

1720

show subpopulations

Gnomad AFR exome

AF:

0.00667

Gnomad AMR exome

AF:

0.155

Gnomad ASJ exome

AF:

0.250

Gnomad EAS exome

AF:

0.800

Gnomad SAS exome

AF:

0.383

Gnomad FIN exome

AF:

0.189

Gnomad NFE exome

AF:

0.218

Gnomad OTH exome

AF:

0.167

GnomAD4 exome

AF:

0.182

AC:

194960

AN:

1072382

Hom.:

20782

Cov.:

AF XY:

0.184

AC XY:

93463

AN XY:

508660

show subpopulations

Gnomad4 AFR exome

AF:

0.0254

Gnomad4 AMR exome

AF:

0.151

Gnomad4 ASJ exome

AF:

0.202

Gnomad4 EAS exome

AF:

0.586

Gnomad4 SAS exome

AF:

0.319

Gnomad4 FIN exome

AF:

0.175

Gnomad4 NFE exome

AF:

0.170

Gnomad4 OTH exome

AF:

0.187

GnomAD4 genome

AF:

0.145

AC:

21783

AN:

149886

Hom.:

2339

Cov.:

AF XY:

0.149

AC XY:

10875

AN XY:

73170

show subpopulations

Gnomad4 AFR

AF:

0.0329

Gnomad4 AMR

AF:

0.134

Gnomad4 ASJ

AF:

0.200

Gnomad4 EAS

AF:

0.527

Gnomad4 SAS

AF:

0.289

Gnomad4 FIN

AF:

0.155

Gnomad4 NFE

AF:

0.172

Gnomad4 OTH

AF:

0.158

Alfa

AF:

0.0796

Hom.:

Bravo

AF:

0.140

Asia WGS

AF:

0.343

AC:

1168

AN:

3414

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Jan 24, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 25% of patients studied by a panel of primary immunodeficiencies. Number of patients: 22. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

DANN

Benign

0.96

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

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