chr19-44329009-T-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_013380.4(ZNF112):c.1148A>T(p.Tyr383Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00155 in 1,613,976 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_013380.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF112 | NM_013380.4 | c.1148A>T | p.Tyr383Phe | missense_variant | 4/4 | ENST00000354340.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF112 | ENST00000354340.9 | c.1148A>T | p.Tyr383Phe | missense_variant | 4/4 | 1 | NM_013380.4 | A2 | |
ZNF112 | ENST00000337401.8 | c.1166A>T | p.Tyr389Phe | missense_variant | 5/5 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00863 AC: 1313AN: 152210Hom.: 20 Cov.: 32
GnomAD3 exomes AF: 0.00203 AC: 508AN: 250260Hom.: 7 AF XY: 0.00157 AC XY: 212AN XY: 135224
GnomAD4 exome AF: 0.000805 AC: 1177AN: 1461648Hom.: 18 Cov.: 69 AF XY: 0.000697 AC XY: 507AN XY: 727112
GnomAD4 genome ? AF: 0.00865 AC: 1317AN: 152328Hom.: 20 Cov.: 32 AF XY: 0.00852 AC XY: 635AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 16, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at