chr6-28365690-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_024493.4(ZKSCAN3):c.1022C>T(p.Pro341Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,256 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024493.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZKSCAN3 | ENST00000252211.7 | c.1022C>T | p.Pro341Leu | missense_variant | Exon 6 of 6 | 1 | NM_024493.4 | ENSP00000252211.2 | ||
ZKSCAN3 | ENST00000377255.3 | c.1022C>T | p.Pro341Leu | missense_variant | Exon 7 of 7 | 1 | ENSP00000366465.1 | |||
ZKSCAN3 | ENST00000341464.9 | c.578C>T | p.Pro193Leu | missense_variant | Exon 5 of 5 | 2 | ENSP00000341883.5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152256Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251216Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135764
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152256Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1022C>T (p.P341L) alteration is located in exon 7 (coding exon 5) of the ZKSCAN3 gene. This alteration results from a C to T substitution at nucleotide position 1022, causing the proline (P) at amino acid position 341 to be replaced by a leucine (L). 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