6-28365902-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024493.4(ZKSCAN3):āc.1234A>Gā(p.Ser412Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,461,008 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_024493.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZKSCAN3 | ENST00000252211.7 | c.1234A>G | p.Ser412Gly | missense_variant | 6/6 | 1 | NM_024493.4 | ENSP00000252211.2 | ||
ZKSCAN3 | ENST00000377255.3 | c.1234A>G | p.Ser412Gly | missense_variant | 7/7 | 1 | ENSP00000366465.1 | |||
ZKSCAN3 | ENST00000341464.9 | c.790A>G | p.Ser264Gly | missense_variant | 5/5 | 2 | ENSP00000341883.5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461008Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 726776
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 14, 2023 | The c.1234A>G (p.S412G) alteration is located in exon 7 (coding exon 5) of the ZKSCAN3 gene. This alteration results from a A to G substitution at nucleotide position 1234, causing the serine (S) at amino acid position 412 to be replaced by a glycine (G). 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.