11-46701082-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS1
The NM_024741.3(ZNF408):āc.35A>Gā(p.Lys12Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000109 in 1,614,154 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_024741.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF408 | ENST00000311764.3 | c.35A>G | p.Lys12Arg | missense_variant | Exon 1 of 5 | 1 | NM_024741.3 | ENSP00000309606.2 | ||
ZNF408 | ENST00000526410.1 | n.52A>G | non_coding_transcript_exon_variant | Exon 1 of 3 | 3 | |||||
ZNF408 | ENST00000531866.1 | n.53A>G | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000565 AC: 86AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000208 AC: 52AN: 249924Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135234
GnomAD4 exome AF: 0.0000616 AC: 90AN: 1461854Hom.: 0 Cov.: 31 AF XY: 0.0000509 AC XY: 37AN XY: 727232
GnomAD4 genome AF: 0.000565 AC: 86AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.000483 AC XY: 36AN XY: 74482
ClinVar
Submissions by phenotype
ZNF408-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at