rs234301
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_178544.5(ZNF546):c.*330A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 279,800 control chromosomes in the GnomAD database, including 5,120 homozygotes. 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: 𝑓 0.16 ( 4534 hom., cov: 32)
Exomes 𝑓: 0.054 ( 586 hom. )
Consequence
ZNF546
NM_178544.5 3_prime_UTR
NM_178544.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.134
Genes affected
ZNF546 (HGNC:28671): (zinc finger protein 546) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be integral component of membrane. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF546 | NM_178544.5 | c.*330A>G | 3_prime_UTR_variant | 7/7 | ENST00000347077.9 | ||
ZNF546 | NM_001297763.2 | c.*330A>G | 3_prime_UTR_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF546 | ENST00000347077.9 | c.*330A>G | 3_prime_UTR_variant | 7/7 | 1 | NM_178544.5 | P2 | ||
ZNF546 | ENST00000600094.5 | c.*330A>G | 3_prime_UTR_variant | 7/7 | 2 | A2 | |||
ZNF546 | ENST00000596894.5 | c.77-317A>G | intron_variant | 3 | |||||
ZNF546 | ENST00000651981.1 | c.*2795A>G | 3_prime_UTR_variant, NMD_transcript_variant | 8/8 |
Frequencies
GnomAD3 genomes ? AF: 0.157 AC: 23790AN: 151522Hom.: 4520 Cov.: 32
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GnomAD4 exome AF: 0.0542 AC: 6948AN: 128162Hom.: 586 Cov.: 0 AF XY: 0.0566 AC XY: 3875AN XY: 68462
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GnomAD4 genome ? AF: 0.157 AC: 23858AN: 151638Hom.: 4534 Cov.: 32 AF XY: 0.155 AC XY: 11476AN XY: 74090
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ClinVar
Not reported inComputational scores
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Name
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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