chr19-53140666-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032584.3(ZNF347):c.2162G>A(p.Arg721His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000258 in 1,602,820 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032584.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF347 | NM_032584.3 | c.2162G>A | p.Arg721His | missense_variant | Exon 5 of 5 | ENST00000334197.12 | NP_115973.2 | |
ZNF347 | NM_001172674.2 | c.2165G>A | p.Arg722His | missense_variant | Exon 5 of 5 | NP_001166145.1 | ||
ZNF347 | NM_001172675.2 | c.2165G>A | p.Arg722His | missense_variant | Exon 5 of 5 | NP_001166146.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF347 | ENST00000334197.12 | c.2162G>A | p.Arg721His | missense_variant | Exon 5 of 5 | 1 | NM_032584.3 | ENSP00000334146.6 | ||
ZNF347 | ENST00000452676.6 | c.2165G>A | p.Arg722His | missense_variant | Exon 5 of 5 | 2 | ENSP00000405218.2 | |||
ZNF347 | ENST00000601469.2 | c.2165G>A | p.Arg722His | missense_variant | Exon 5 of 5 | 2 | ENSP00000471712.2 | |||
ZNF347 | ENST00000601804.5 | c.97+8015G>A | intron_variant | Intron 3 of 3 | 4 | ENSP00000470590.1 |
Frequencies
GnomAD3 genomes AF: 0.000224 AC: 32AN: 142920Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000217 AC: 54AN: 248746Hom.: 0 AF XY: 0.000223 AC XY: 30AN XY: 134518
GnomAD4 exome AF: 0.000257 AC: 375AN: 1459766Hom.: 0 Cov.: 31 AF XY: 0.000238 AC XY: 173AN XY: 726170
GnomAD4 genome AF: 0.000273 AC: 39AN: 143054Hom.: 1 Cov.: 33 AF XY: 0.000244 AC XY: 17AN XY: 69564
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2165G>A (p.R722H) alteration is located in exon 5 (coding exon 4) of the ZNF347 gene. This alteration results from a G to A substitution at nucleotide position 2165, causing the arginine (R) at amino acid position 722 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