Variant 20-33788942-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2

The NM_001282933.2(ZNF341):c.1932C>T(p.His644=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0195 in 1,613,978 control chromosomes in the GnomAD database, including 375 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.015 ( 31 hom., cov: 32)

Exomes 𝑓: 0.020 ( 344 hom. )

Consequence

ZNF341
NM_001282933.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.255

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:

ZNF341-AS1 (HGNC:50736): (ZNF341 antisense RNA 1)

ZNF341-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.29).

BP6

Variant 20-33788942-C-T is Benign according to our data. Variant chr20-33788942-C-T is described in ClinVar as [Benign]. Clinvar id is 1169237.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.255 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0152 (2314/152260) while in subpopulation NFE AF= 0.0231 (1573/68020). AF 95% confidence interval is 0.0222. There are 31 homozygotes in gnomad4. There are 1114 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 31 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF341	NM_001282933.2 linkuse as main transcript	c.1932C>T	p.His644=	synonymous_variant	13/15	ENST00000375200.6	NP_001269862.1
ZNF341-AS1	NR_110623.1 linkuse as main transcript	n.242-1165G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF341	ENST00000375200.6 linkuse as main transcript	c.1932C>T	p.His644=	synonymous_variant	13/15	1	NM_001282933.2	ENSP00000364346	P4	Q9BYN7-1
ZNF341-AS1	ENST00000443171.6 linkuse as main transcript	n.252-1165G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0152

AC:

2316

AN:

152142

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00326

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0211

Gnomad ASJ

AF:

0.0112

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0201

Gnomad FIN

AF:

0.00840

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0231

Gnomad OTH

AF:

0.0215

GnomAD3 exomes

AF:

0.0168

AC:

4216

AN:

251300

Hom.:

AF XY:

0.0183

AC XY:

2486

AN XY:

135872

show subpopulations

Gnomad AFR exome

AF:

0.00252

Gnomad AMR exome

AF:

0.0129

Gnomad ASJ exome

AF:

0.0126

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0210

Gnomad FIN exome

AF:

0.00822

Gnomad NFE exome

AF:

0.0234

Gnomad OTH exome

AF:

0.0187

GnomAD4 exome

AF:

0.0199

AC:

29092

AN:

1461718

Hom.:

344

Cov.:

AF XY:

0.0201

AC XY:

14591

AN XY:

727142

show subpopulations

Gnomad4 AFR exome

AF:

0.00349

Gnomad4 AMR exome

AF:

0.0131

Gnomad4 ASJ exome

AF:

0.0103

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.0220

Gnomad4 FIN exome

AF:

0.00769

Gnomad4 NFE exome

AF:

0.0221

Gnomad4 OTH exome

AF:

0.0176

GnomAD4 genome

AF:

0.0152

AC:

2314

AN:

152260

Hom.:

Cov.:

AF XY:

0.0150

AC XY:

1114

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.00325

Gnomad4 AMR

AF:

0.0211

Gnomad4 ASJ

AF:

0.0112

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0203

Gnomad4 FIN

AF:

0.00840

Gnomad4 NFE

AF:

0.0231

Gnomad4 OTH

AF:

0.0208

Alfa

AF:

0.0183

Hom.:

Bravo

AF:

0.0153

Asia WGS

AF:

0.00462

AC:

AN:

3478

EpiCase

AF:

0.0251

EpiControl

AF:

0.0236

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

ZNF341-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 26, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.29

CADD

Benign

7.5

DANN

Benign

0.90

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