NM_001282933.2:c.31+18C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001282933.2(ZNF341):​c.31+18C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000009 in 1,111,386 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 9.0e-7 ( 0 hom. )

Consequence

ZNF341
NM_001282933.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.392

Publications

0 publications found
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 Gene-Disease associations (from GenCC):
  • hyper-IgE recurrent infection syndrome 3, autosomal recessive
    Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZNF341NM_001282933.2 linkc.31+18C>A intron_variant Intron 1 of 14 ENST00000375200.6 NP_001269862.1 Q9BYN7-1Q504V9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF341ENST00000375200.6 linkc.31+18C>A intron_variant Intron 1 of 14 1 NM_001282933.2 ENSP00000364346.1 Q9BYN7-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD2 exomes
AF:
0.00
AC:
0
AN:
5644
AF XY:
0.00
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
9.00e-7
AC:
1
AN:
1111386
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
531548
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
22616
American (AMR)
AF:
0.00
AC:
0
AN:
8272
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
14486
East Asian (EAS)
AF:
0.0000380
AC:
1
AN:
26332
South Asian (SAS)
AF:
0.00
AC:
0
AN:
32644
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
28504
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3156
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
931296
Other (OTH)
AF:
0.00
AC:
0
AN:
44080
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.72
CADD
Benign
17
DANN
Benign
0.82
PhyloP100
-0.39
PromoterAI
0.053
Neutral
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.3

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

Other links and lift over

dbSNP: rs1168161710; hg19: chr20-32319876; API