Genetic Variant ZNF341:p.Ile643Ile (chr20-33788939-C-T) – ACMG Classification: Benign (-19 pts)

Variant summary

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

The NM_001282933.2(ZNF341):c.1929C>T(p.Ile643Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0231 in 1,614,028 control chromosomes in the GnomAD database, including 475 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.016 ( 31 hom., cov: 32)

Exomes 𝑓: 0.024 ( 444 hom. )

Consequence

ZNF341
NM_001282933.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 2.60

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=-0.24).

BP6

Variant 20-33788939-C-T is Benign according to our data. Variant chr20-33788939-C-T is described in ClinVar as [Benign]. Clinvar id is 1170037.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.6 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0161 (2459/152288) while in subpopulation NFE AF= 0.0255 (1735/68026). AF 95% confidence interval is 0.0245. There are 31 homozygotes in gnomad4. There are 1144 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 rank	MANE	Protein	UniProt
ZNF341	NM_001282933.2 link	c.1929C>T	p.Ile643Ile	synonymous_variant	Exon 13 of 15	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.1929C>T	p.Ile643Ile	synonymous_variant	Exon 13 of 15	1	NM_001282933.2	ENSP00000364346.1		Q9BYN7-1

Frequencies

GnomAD3 genomes

AF:

0.0161

AC:

2457

AN:

152170

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00393

Gnomad AMI

AF:

0.0757

Gnomad AMR

AF:

0.0132

Gnomad ASJ

AF:

0.0133

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00580

Gnomad FIN

AF:

0.0156

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0255

Gnomad OTH

AF:

0.0210

GnomAD3 exomes

AF:

0.0182

AC:

4582

AN:

251326

Hom.:

AF XY:

0.0184

AC XY:

2501

AN XY:

135880

show subpopulations

Gnomad AFR exome

AF:

0.00455

Gnomad AMR exome

AF:

0.0119

Gnomad ASJ exome

AF:

0.0167

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00715

Gnomad FIN exome

AF:

0.0172

Gnomad NFE exome

AF:

0.0282

Gnomad OTH exome

AF:

0.0209

GnomAD4 exome

AF:

0.0239

AC:

34872

AN:

1461740

Hom.:

444

Cov.:

AF XY:

0.0234

AC XY:

16991

AN XY:

727162

show subpopulations

Gnomad4 AFR exome

AF:

0.00358

Gnomad4 AMR exome

AF:

0.0126

Gnomad4 ASJ exome

AF:

0.0173

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00781

Gnomad4 FIN exome

AF:

0.0187

Gnomad4 NFE exome

AF:

0.0278

Gnomad4 OTH exome

AF:

0.0187

GnomAD4 genome

AF:

0.0161

AC:

2459

AN:

152288

Hom.:

Cov.:

AF XY:

0.0154

AC XY:

1144

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00392

Gnomad4 AMR

AF:

0.0132

Gnomad4 ASJ

AF:

0.0133

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00601

Gnomad4 FIN

AF:

0.0156

Gnomad4 NFE

AF:

0.0255

Gnomad4 OTH

AF:

0.0208

Alfa

AF:

0.0218

Hom.:

Bravo

AF:

0.0163

Asia WGS

AF:

0.00404

AC:

AN:

3478

EpiCase

AF:

0.0237

EpiControl

AF:

0.0261

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

ZNF341-related disorder

Benign:1

Mar 22, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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

-0.24

CADD

Benign

DANN

Benign

0.91

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