chr6-28148447-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006298.4(ZKSCAN8):c.40C>T(p.Pro14Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,860 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_006298.4 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 |
---|---|---|---|---|---|---|---|
ZKSCAN8 | NM_006298.4 | c.40C>T | p.Pro14Ser | missense_variant | 2/6 | ENST00000330236.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZKSCAN8 | ENST00000330236.7 | c.40C>T | p.Pro14Ser | missense_variant | 2/6 | 1 | NM_006298.4 | P1 | |
ZKSCAN8 | ENST00000457389.6 | c.40C>T | p.Pro14Ser | missense_variant | 3/7 | 1 | P1 | ||
ZKSCAN8 | ENST00000606198.5 | c.40C>T | p.Pro14Ser | missense_variant, NMD_transcript_variant | 2/6 | 1 | |||
ZKSCAN8 | ENST00000536028.2 | c.40C>T | p.Pro14Ser | missense_variant, NMD_transcript_variant | 3/7 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461860Hom.: 0 Cov.: 30 AF XY: 0.00000825 AC XY: 6AN XY: 727224
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 18, 2023 | The c.40C>T (p.P14S) alteration is located in exon 2 (coding exon 1) of the ZKSCAN8 gene. This alteration results from a C to T substitution at nucleotide position 40, causing the proline (P) at amino acid position 14 to be replaced by a serine (S). 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
Publications
No publications associated with this variant yet.