11-46701118-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001184751.2(ZNF408):c.5C>T(p.Ser2Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,942 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 5/5 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001184751.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF408 | ENST00000311764.3 | c.52+19C>T | intron_variant | Intron 1 of 4 | 1 | NM_024741.3 | ENSP00000309606.2 | |||
ZNF408 | ENST00000526410.1 | n.69+19C>T | intron_variant | Intron 1 of 2 | 3 | |||||
ZNF408 | ENST00000531866.1 | n.70+19C>T | intron_variant | Intron 1 of 1 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000602 AC: 15AN: 249164Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134914
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461754Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727184
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152188Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at