16-49635950-G-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001379286.1(ZNF423):c.3226C>A(p.Leu1076Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000663 in 1,595,168 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001379286.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF423 | NM_001379286.1 | c.3226C>A | p.Leu1076Met | missense_variant | Exon 4 of 8 | ENST00000563137.7 | NP_001366215.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF423 | ENST00000563137.7 | c.3226C>A | p.Leu1076Met | missense_variant | Exon 4 of 8 | 5 | NM_001379286.1 | ENSP00000455588.3 |
Frequencies
GnomAD3 genomes AF: 0.00372 AC: 566AN: 152218Hom.: 5 Cov.: 33
GnomAD3 exomes AF: 0.000956 AC: 225AN: 235450Hom.: 1 AF XY: 0.000505 AC XY: 64AN XY: 126856
GnomAD4 exome AF: 0.000342 AC: 494AN: 1442832Hom.: 7 Cov.: 31 AF XY: 0.000253 AC XY: 181AN XY: 715138
GnomAD4 genome AF: 0.00370 AC: 563AN: 152336Hom.: 5 Cov.: 33 AF XY: 0.00360 AC XY: 268AN XY: 74484
ClinVar
Submissions by phenotype
Nephronophthisis 14 Benign:2
- -
- -
not provided Benign:2
- -
ZNF423: BS1, BS2 -
not specified Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at