chr6-28153841-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006298.4(ZKSCAN8):c.1561A>G(p.Lys521Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,614,074 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006298.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZKSCAN8 | NM_006298.4 | c.1561A>G | p.Lys521Glu | missense_variant | 6/6 | ENST00000330236.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZKSCAN8 | ENST00000330236.7 | c.1561A>G | p.Lys521Glu | missense_variant | 6/6 | 1 | NM_006298.4 | P1 | |
ZKSCAN8 | ENST00000457389.6 | c.1561A>G | p.Lys521Glu | missense_variant | 7/7 | 1 | P1 | ||
ZKSCAN8 | ENST00000606198.5 | c.*1098A>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251274Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135804
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461854Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727230
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2021 | The c.1561A>G (p.K521E) alteration is located in exon 6 (coding exon 5) of the ZKSCAN8 gene. This alteration results from a A to G substitution at nucleotide position 1561, causing the lysine (K) at amino acid position 521 to be replaced by a glutamic acid (E). 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