chr20-33732064-C-CGGGGCCGGCGGA

Variant names:

• chr20-33732064-C-CGGGGCCGGCGGA
• NM_001282933.2:c.31+15_31+26dupGGCCGGCGGAGG

Variant summary

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

The NM_001282933.2(ZNF341):​c.31+15_31+26dupGGCCGGCGGAGG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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)
• Consequence: ZNF341 NM_001282933.2 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0980
• 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: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen

ENSG00000229188 (HGNC:):

ACMG classification

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

• BP6: Variant 20-33732064-C-CGGGGCCGGCGGA is Benign according to our data. Variant chr20-33732064-C-CGGGGCCGGCGGA is described in ClinVar as Likely_benign. ClinVar VariationId is 2816513.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001282933.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF341	NM_001282933.2	MANE Select	c.31+15_31+26dupGGCCGGCGGAGG		intron	N/A	NP_001269862.1	Q9BYN7-1
	ZNF341	NM_032819.5		c.31+15_31+26dupGGCCGGCGGAGG		intron	N/A	NP_116208.3
	ZNF341	NM_001282935.2		c.-43+15_-43+26dupGGCCGGCGGAGG		intron	N/A	NP_001269864.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF341	ENST00000375200.6	TSL:1 MANE Select	c.31+12_31+13insGGGGCCGGCGGA		intron	N/A	ENSP00000364346.1	Q9BYN7-1
	ZNF341	ENST00000342427.6	TSL:1	c.31+12_31+13insGGGGCCGGCGGA		intron	N/A	ENSP00000344308.2	Q9BYN7-2
	ZNF341	ENST00000483118.5	TSL:1	n.31+12_31+13insGGGGCCGGCGGA		intron	N/A	ENSP00000432933.1	E9PN62

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 31

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.098

Splicing

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

Other links and lift over

hg19: chr20-32319870;