chr6-28148532-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_006298.4(ZKSCAN8):c.125G>A(p.Ser42Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000039 in 1,614,178 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006298.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZKSCAN8 | NM_006298.4 | c.125G>A | p.Ser42Asn | missense_variant | 2/6 | ENST00000330236.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZKSCAN8 | ENST00000330236.7 | c.125G>A | p.Ser42Asn | missense_variant | 2/6 | 1 | NM_006298.4 | P1 | |
ZKSCAN8 | ENST00000457389.6 | c.125G>A | p.Ser42Asn | missense_variant | 3/7 | 1 | P1 | ||
ZKSCAN8 | ENST00000606198.5 | c.125G>A | p.Ser42Asn | missense_variant, NMD_transcript_variant | 2/6 | 1 | |||
ZKSCAN8 | ENST00000536028.2 | c.125G>A | p.Ser42Asn | missense_variant, NMD_transcript_variant | 3/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000636 AC: 16AN: 251496Hom.: 1 AF XY: 0.0000368 AC XY: 5AN XY: 135922
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461894Hom.: 1 Cov.: 30 AF XY: 0.0000179 AC XY: 13AN XY: 727248
GnomAD4 genome ? AF: 0.000217 AC: 33AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74450
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 10, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at