chr19-44328890-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_013380.4(ZNF112):c.1267A>T(p.Asn423Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,706 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013380.4 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 |
---|---|---|---|---|---|---|---|
ZNF112 | NM_013380.4 | c.1267A>T | p.Asn423Tyr | missense_variant | 4/4 | ENST00000354340.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF112 | ENST00000354340.9 | c.1267A>T | p.Asn423Tyr | missense_variant | 4/4 | 1 | NM_013380.4 | A2 | |
ZNF112 | ENST00000337401.8 | c.1285A>T | p.Asn429Tyr | missense_variant | 5/5 | 1 | P4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250218Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135244
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461706Hom.: 0 Cov.: 69 AF XY: 0.00 AC XY: 0AN XY: 727156
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | The c.1285A>T (p.N429Y) alteration is located in exon 5 (coding exon 4) of the ZNF112 gene. This alteration results from a A to T substitution at nucleotide position 1285, causing the asparagine (N) at amino acid position 429 to be replaced by a tyrosine (Y). 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