19-43873004-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001033719.3(ZNF404):c.1210A>T(p.Ile404Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000058 in 1,602,688 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_001033719.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000362 AC: 55AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000608 AC: 14AN: 230392Hom.: 0 AF XY: 0.0000402 AC XY: 5AN XY: 124380
GnomAD4 exome AF: 0.0000262 AC: 38AN: 1450444Hom.: 0 Cov.: 35 AF XY: 0.0000153 AC XY: 11AN XY: 720552
GnomAD4 genome AF: 0.000361 AC: 55AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74438
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 25, 2024 | The c.1210A>T (p.I404F) alteration is located in exon 3 (coding exon 3) of the ZNF404 gene. This alteration results from a A to T substitution at nucleotide position 1210, causing the isoleucine (I) at amino acid position 404 to be replaced by a phenylalanine (F). 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