19-11780383-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152355.3(ZNF441):āc.559A>Gā(p.Met187Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,614,138 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_152355.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF441 | NM_152355.3 | c.559A>G | p.Met187Val | missense_variant | 4/4 | ENST00000357901.5 | NP_689568.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF441 | ENST00000357901.5 | c.559A>G | p.Met187Val | missense_variant | 4/4 | 3 | NM_152355.3 | ENSP00000350576 | P1 | |
ZNF441 | ENST00000409902.5 | c.*488A>G | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 2 | ENSP00000386658 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152272Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251270Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135780
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461866Hom.: 0 Cov.: 34 AF XY: 0.0000165 AC XY: 12AN XY: 727232
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152272Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74394
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2023 | The c.559A>G (p.M187V) alteration is located in exon 4 (coding exon 4) of the ZNF441 gene. This alteration results from a A to G substitution at nucleotide position 559, causing the methionine (M) at amino acid position 187 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at