Variant 20-33745375-G-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001282933.2(ZNF341):c.339+76G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 1,438,444 control chromosomes in the GnomAD database, including 45,560 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.23 ( 4406 hom., cov: 32)

Exomes 𝑓: 0.25 ( 41154 hom. )

Consequence

ZNF341
NM_001282933.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.338

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:

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=-0.84).

BP6

Variant 20-33745375-G-T is Benign according to our data. Variant chr20-33745375-G-T is described in ClinVar as [Benign]. Clinvar id is 2628155.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
ZNF341	NM_001282933.2 link	c.339+76G>T	intron_variant	ENST00000375200.6	NP_001269862.1	Q9BYN7-1Q504V9
ZNF341	NM_032819.5 link	c.339+76G>T	intron_variant		NP_116208.3	Q9BYN7-2Q504V9
ZNF341	NM_001282935.2 link	c.70-3548G>T	intron_variant		NP_001269864.1	Q9BYN7Q504V9
ZNF341	NR_104259.2 link	n.365+76G>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF341	ENST00000375200.6 link	c.339+76G>T		intron_variant		1	NM_001282933.2	ENSP00000364346.1		Q9BYN7-1

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35686

AN:

151988

Hom.:

4403

Cov.:

show subpopulations

Gnomad AFR

AF:

0.194

Gnomad AMI

AF:

0.240

Gnomad AMR

AF:

0.315

Gnomad ASJ

AF:

0.214

Gnomad EAS

AF:

0.241

Gnomad SAS

AF:

0.189

Gnomad FIN

AF:

0.239

Gnomad MID

AF:

0.229

Gnomad NFE

AF:

0.245

Gnomad OTH

AF:

0.228

GnomAD4 exome

AF:

0.249

AC:

320005

AN:

1286338

Hom.:

41154

AF XY:

0.247

AC XY:

155889

AN XY:

632396

show subpopulations

Gnomad4 AFR exome

AF:

0.196

Gnomad4 AMR exome

AF:

0.390

Gnomad4 ASJ exome

AF:

0.204

Gnomad4 EAS exome

AF:

0.221

Gnomad4 SAS exome

AF:

0.194

Gnomad4 FIN exome

AF:

0.230

Gnomad4 NFE exome

AF:

0.253

Gnomad4 OTH exome

AF:

0.248

GnomAD4 genome

AF:

0.235

AC:

35712

AN:

152106

Hom.:

4406

Cov.:

AF XY:

0.235

AC XY:

17474

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.194

Gnomad4 AMR

AF:

0.315

Gnomad4 ASJ

AF:

0.214

Gnomad4 EAS

AF:

0.240

Gnomad4 SAS

AF:

0.190

Gnomad4 FIN

AF:

0.239

Gnomad4 NFE

AF:

0.245

Gnomad4 OTH

AF:

0.227

Alfa

AF:

0.242

Hom.:

10431

Bravo

AF:

0.243

Asia WGS

AF:

0.218

AC:

758

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Nov 12, 2023

This variant is classified as Benign based on local population frequency. This variant was detected in 55% of patients studied by a panel of primary immunodeficiencies. Number of patients: 53. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.90

DANN

Benign

0.49

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