chr15-55418091-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001033560.2(DNAAF4):c.1090C>T(p.Pro364Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000142 in 1,580,710 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001033560.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIERCE2 | NM_001198784.2 | c.19-132G>A | intron_variant | Intron 1 of 1 | ENST00000569691.2 | NP_001185713.1 | ||
DNAAF4 | NM_001033560.2 | c.1090C>T | p.Pro364Ser | missense_variant | Exon 9 of 9 | NP_001028732.1 | ||
DNAAF4-CCPG1 | NR_037923.1 | n.1408+14406C>T | intron_variant | Intron 8 of 15 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000223 AC: 49AN: 220140Hom.: 0 AF XY: 0.000218 AC XY: 26AN XY: 119340
GnomAD4 exome AF: 0.000144 AC: 205AN: 1428522Hom.: 2 Cov.: 28 AF XY: 0.000173 AC XY: 123AN XY: 710242
GnomAD4 genome AF: 0.000131 AC: 20AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74346
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | DNAAF4: PM2, BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at