chr11-46701095-A-G
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_024741.3(ZNF408):āc.48A>Gā(p.Gln16=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,613,932 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.000013 ( 0 hom., cov: 33)
Exomes š: 0.000026 ( 0 hom. )
Consequence
ZNF408
NM_024741.3 synonymous
NM_024741.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.116
Genes affected
ZNF408 (HGNC:20041): (zinc finger protein 408) The protein encoded by this gene contains ten tandem zinc fingers and an N-terminal SET domain, so it is likely a DNA binding protein that interacts with other proteins. In adults, the encoded protein is expressed most highly in retina. Consequently, defects in this gene have been associated with familial exudative vitreoretinopathy (FEVR) and retinitis pigmentosa (RP). [provided by RefSeq, Dec 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
Variant 11-46701095-A-G is Benign according to our data. Variant chr11-46701095-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1624752.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.116 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF408 | NM_024741.3 | c.48A>G | p.Gln16= | synonymous_variant | 1/5 | ENST00000311764.3 | |
ZNF408 | NM_001184751.2 | c.-19A>G | 5_prime_UTR_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF408 | ENST00000311764.3 | c.48A>G | p.Gln16= | synonymous_variant | 1/5 | 1 | NM_024741.3 | P1 | |
ZNF408 | ENST00000526410.1 | n.65A>G | non_coding_transcript_exon_variant | 1/3 | 3 | ||||
ZNF408 | ENST00000531866.1 | n.66A>G | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152104Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000601 AC: 15AN: 249648Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135124
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GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461828Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 727216
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152104Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74282
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at