chr19-21972110-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007153.3(ZNF208):c.2924A>G(p.Tyr975Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000158 in 1,459,856 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_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.2924A>G | p.Tyr975Cys | missense_variant | 4/4 | ENST00000397126.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF208 | ENST00000397126.9 | c.2924A>G | p.Tyr975Cys | missense_variant | 4/4 | 3 | NM_007153.3 | P1 | |
ZNF208 | ENST00000599916.5 | c.305+2619A>G | intron_variant | 1 | |||||
ZNF208 | ENST00000601773.5 | c.226+15106A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 5AN: 148722Hom.: 0 Cov.: 33 FAILED QC
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247608Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134310
GnomAD4 exome AF: 0.0000158 AC: 23AN: 1459856Hom.: 0 Cov.: 113 AF XY: 0.0000124 AC XY: 9AN XY: 726266
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000336 AC: 5AN: 148850Hom.: 0 Cov.: 33 AF XY: 0.0000275 AC XY: 2AN XY: 72692
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.2924A>G (p.Y975C) 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 2924, causing the tyrosine (Y) at amino acid position 975 to be replaced by a cysteine (C). 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