chr19-21971319-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007153.3(ZNF208):āc.3715A>Gā(p.Ile1239Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,611,488 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 (ā ).
Frequency
Consequence
NM_007153.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF208 | NM_007153.3 | c.3715A>G | p.Ile1239Val | missense_variant | 4/4 | ENST00000397126.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF208 | ENST00000397126.9 | c.3715A>G | p.Ile1239Val | missense_variant | 4/4 | 3 | NM_007153.3 | P1 | |
ZNF208 | ENST00000599916.5 | c.305+3410A>G | intron_variant | 1 | |||||
ZNF208 | ENST00000601773.5 | c.226+15897A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151714Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 244314Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133024
GnomAD4 exome AF: 0.0000370 AC: 54AN: 1459652Hom.: 0 Cov.: 125 AF XY: 0.0000358 AC XY: 26AN XY: 726186
GnomAD4 genome AF: 0.0000395 AC: 6AN: 151836Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74230
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2023 | The c.3715A>G (p.I1239V) alteration is located in exon 4 (coding exon 4) of the ZNF208 gene. This alteration results from a A to G substitution at nucleotide position 3715, causing the isoleucine (I) at amino acid position 1239 to be replaced by a valine (V). 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