chr19-47544921-C-T
Position:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001277075.3(ZNF541):c.1608G>A(p.Pro536=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000723 in 1,383,566 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 7.2e-7 ( 0 hom. )
Consequence
ZNF541
NM_001277075.3 synonymous
NM_001277075.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.88
Genes affected
ZNF541 (HGNC:25294): (zinc finger protein 541) Predicted to enable transcription corepressor activity. Predicted to be involved in histone deacetylation; negative regulation of transcription, DNA-templated; and regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be part of histone deacetylase complex and transcription regulator complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP7
Synonymous conserved (PhyloP=-5.88 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| ZNF541 | NM_001277075.3 | c.1608G>A | p.Pro536= | synonymous_variant | 5/17 | ENST00000391901.8 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ZNF541 | ENST00000391901.8 | c.1608G>A | p.Pro536= | synonymous_variant | 5/17 | 5 | NM_001277075.3 | P1 | |
| ZNF541 | ENST00000595558.1 | c.342G>A | p.Pro114= | synonymous_variant | 1/12 | 1 | |||
| ZNF541 | ENST00000263351.9 | c.381G>A | p.Pro127= | synonymous_variant | 1/7 | 1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 7.23e-7 AC: 1AN: 1383566Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 682690
GnomAD4 exome
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1
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1383566
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33
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0
AN XY:
682690
Gnomad4 AFR exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not provided Uncertain:1
| Uncertain significance, no assertion criteria provided | literature only | Richard Lifton Laboratory, Yale University School of Medicine | - | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at