20-33732057-G-GCGGCGGCGGGGC

Variant names:

• chr20-33732057-G-GCGGCGGCGGGGC
• NM_001282933.2:c.31+12_31+23dupCGGGGCCGGCGG

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The ENST00000375200.6(ZNF341):​c.31+5_31+6insCGGCGGCGGGGC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000176 in 1,134,892 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0000018 (0 hom.)
• Consequence: ZNF341 ENST00000375200.6 splice_region, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.378
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• hyper-IgE recurrent infection syndrome 3, autosomal recessive

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

ENSG00000229188 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP6: Variant 20-33732057-G-GCGGCGGCGGGGC is Benign according to our data. Variant chr20-33732057-G-GCGGCGGCGGGGC is described in ClinVar as [Likely_benign]. Clinvar id is 2965828.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF341	NM_001282933.2	c.31+12_31+23dupCGGGGCCGGCGG		intron_variant	Intron 1 of 14	ENST00000375200.6	NP_001269862.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF341	ENST00000375200.6	c.31+5_31+6insCGGCGGCGGGGC		splice_region_variant, intron_variant	Intron 1 of 14	1	NM_001282933.2	ENSP00000364346.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000176 AC: 2 AN: 1134892 Hom.: 0 Cov.: 30 AF XY: 0.00000367 AC XY: 2 AN XY: 545102

African (AFR) AF: 0.00 AC: 0 AN: 23024

American (AMR) AF: 0.00 AC: 0 AN: 9010

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15374

East Asian (EAS) AF: 0.00 AC: 0 AN: 26754

South Asian (SAS) AF: 0.00 AC: 0 AN: 36608

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31996

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3454

European-Non Finnish (NFE) AF: 0.00000212 AC: 2 AN: 943502

Other (OTH) AF: 0.00 AC: 0 AN: 45170

GnomAD4 genome Cov.: 31

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Apr 30, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

hg19: chr20-32319863;