19-57978584-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001348022.3(ZNF606):c.2096G>A(p.Arg699Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,613,340 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R699W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001348022.3 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 |
---|---|---|---|---|---|---|---|
ZNF606 | NM_001348022.3 | c.2096G>A | p.Arg699Gln | missense_variant | 7/7 | ENST00000551380.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF606 | ENST00000551380.7 | c.2096G>A | p.Arg699Gln | missense_variant | 7/7 | 5 | NM_001348022.3 | P1 | |
ZNF606 | ENST00000341164.9 | c.2096G>A | p.Arg699Gln | missense_variant | 7/7 | 1 | P1 | ||
ZNF606 | ENST00000550599.6 | c.*1830G>A | 3_prime_UTR_variant, NMD_transcript_variant | 6/6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000264 AC: 4AN: 151688Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251204Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135782
GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461652Hom.: 1 Cov.: 31 AF XY: 0.0000619 AC XY: 45AN XY: 727106
GnomAD4 genome AF: 0.0000264 AC: 4AN: 151688Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74078
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at