7-149178878-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_170686.3(ZNF398):c.1006C>A(p.Pro336Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,998 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF398 | NM_170686.3 | c.1006C>A | p.Pro336Thr | missense_variant | 6/6 | ENST00000475153.6 | NP_733787.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF398 | ENST00000475153.6 | c.1006C>A | p.Pro336Thr | missense_variant | 6/6 | 1 | NM_170686.3 | ENSP00000420418.1 | ||
ZNF398 | ENST00000426851.6 | c.493C>A | p.Pro165Thr | missense_variant | 7/7 | 1 | ENSP00000389972.2 | |||
ZNF398 | ENST00000483892.5 | c.493C>A | p.Pro165Thr | missense_variant | 6/6 | 5 | ENSP00000418564.1 | |||
ZNF398 | ENST00000491174.1 | c.493C>A | p.Pro165Thr | missense_variant | 7/7 | 2 | ENSP00000419391.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251370Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135850
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461808Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727196
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2023 | The c.1006C>A (p.P336T) alteration is located in exon 6 (coding exon 6) of the ZNF398 gene. This alteration results from a C to A substitution at nucleotide position 1006, causing the proline (P) at amino acid position 336 to be replaced by a threonine (T). 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