chr16-71475210-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006961.4(ZNF19):c.1337G>A(p.Arg446His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,612,632 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R446S) has been classified as Uncertain significance.
Frequency
Consequence
NM_006961.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF19 | ENST00000288177.10 | c.1337G>A | p.Arg446His | missense_variant | Exon 6 of 6 | 1 | NM_006961.4 | ENSP00000288177.5 | ||
ENSG00000261611 | ENST00000561908.1 | n.274+3018G>A | intron_variant | Intron 5 of 11 | 2 | ENSP00000463741.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 247518Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133868
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1460462Hom.: 0 Cov.: 29 AF XY: 0.0000165 AC XY: 12AN XY: 726352
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1337G>A (p.R446H) alteration is located in exon 6 (coding exon 4) of the ZNF19 gene. This alteration results from a G to A substitution at nucleotide position 1337, causing the arginine (R) at amino acid position 446 to be replaced by a histidine (H). 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