19-21183385-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_133473.4(ZNF431):c.1082A>C(p.Lys361Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00133 in 1,612,754 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 (★).
Frequency
Consequence
NM_133473.4 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 | UniProt |
---|---|---|---|---|---|---|---|
ZNF431 | NM_133473.4 | c.1082A>C | p.Lys361Thr | missense_variant | 5/5 | ENST00000311048.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF431 | ENST00000311048.11 | c.1082A>C | p.Lys361Thr | missense_variant | 5/5 | 1 | NM_133473.4 | P1 | |
ZNF431 | ENST00000600692.5 | c.*669A>C | 3_prime_UTR_variant | 6/6 | 5 | ||||
ZNF431 | ENST00000594425.5 | c.97-6480A>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000773 AC: 117AN: 151412Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000627 AC: 156AN: 248870Hom.: 0 AF XY: 0.000564 AC XY: 76AN XY: 134760
GnomAD4 exome AF: 0.00139 AC: 2034AN: 1461342Hom.: 0 Cov.: 31 AF XY: 0.00127 AC XY: 923AN XY: 726962
GnomAD4 genome ? AF: 0.000773 AC: 117AN: 151412Hom.: 0 Cov.: 33 AF XY: 0.000757 AC XY: 56AN XY: 73948
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.1082A>C (p.K361T) alteration is located in exon 5 (coding exon 5) of the ZNF431 gene. This alteration results from a A to C substitution at nucleotide position 1082, causing the lysine (K) at amino acid position 361 to be replaced by a threonine (T). 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