chr7-149178983-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_170686.3(ZNF398):c.1111C>T(p.Pro371Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF398 | NM_170686.3 | c.1111C>T | p.Pro371Ser | missense_variant | 6/6 | ENST00000475153.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF398 | ENST00000475153.6 | c.1111C>T | p.Pro371Ser | missense_variant | 6/6 | 1 | NM_170686.3 | P1 | |
ZNF398 | ENST00000426851.6 | c.598C>T | p.Pro200Ser | missense_variant | 7/7 | 1 | |||
ZNF398 | ENST00000483892.5 | c.598C>T | p.Pro200Ser | missense_variant | 6/6 | 5 | |||
ZNF398 | ENST00000491174.1 | c.598C>T | p.Pro200Ser | missense_variant | 7/7 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461888Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727246
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 21, 2022 | The c.1111C>T (p.P371S) 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 1111, causing the proline (P) at amino acid position 371 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.