chr16-3137609-C-T
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_004220.3(ZNF213):c.329C>T(p.Pro110Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,922 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004220.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF213 | NM_004220.3 | c.329C>T | p.Pro110Leu | missense_variant | Exon 2 of 6 | ENST00000396878.8 | NP_004211.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152142Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000359 AC: 9AN: 250544 AF XY: 0.0000516 show subpopulations
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461662Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727140 show subpopulations
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152260Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74438 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.329C>T (p.P110L) alteration is located in exon 2 (coding exon 1) of the ZNF213 gene. This alteration results from a C to T substitution at nucleotide position 329, causing the proline (P) at amino acid position 110 to be replaced by a leucine (L). 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