chr7-149179100-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_170686.3(ZNF398):c.1228C>T(p.Pro410Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,613,992 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_170686.3 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 |
---|---|---|---|---|---|---|---|
ZNF398 | NM_170686.3 | c.1228C>T | p.Pro410Ser | missense_variant | 6/6 | ENST00000475153.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF398 | ENST00000475153.6 | c.1228C>T | p.Pro410Ser | missense_variant | 6/6 | 1 | NM_170686.3 | P1 | |
ZNF398 | ENST00000426851.6 | c.715C>T | p.Pro239Ser | missense_variant | 7/7 | 1 | |||
ZNF398 | ENST00000483892.5 | c.715C>T | p.Pro239Ser | missense_variant | 6/6 | 5 | |||
ZNF398 | ENST00000491174.1 | c.715C>T | p.Pro239Ser | missense_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251214Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135768
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461888Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 727244
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152104Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74286
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 30, 2023 | The c.1228C>T (p.P410S) alteration is located in exon 6 (coding exon 6) of the ZNF398 gene. This alteration results from a C to T substitution at nucleotide position 1228, causing the proline (P) at amino acid position 410 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