5-73447202-GGCGGCGGCGGCCTGC-GGCGGCGGCGGCCTGCGCGGCGGCGGCCTGC
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4BS2
The NM_004472.3(FOXD1):c.1146_1160dupGCAGGCCGCCGCCGC(p.Ala387_Ala388insGlnAlaAlaAlaAla) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000117 in 992,660 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000069 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00013 ( 0 hom. )
Consequence
FOXD1
NM_004472.3 disruptive_inframe_insertion
NM_004472.3 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.257
Genes affected
FOXD1 (HGNC:3802): (forkhead box D1) This gene belongs to the forkhead family of transcription factors which are characterized by a distinct forkhead domain. Studies of the orthologous mouse protein indicate that it functions in kidney development by promoting nephron progenitor differentiation, and it also functions in the development of the retina and optic chiasm. It may also regulate inflammatory reactions and prevent autoimmunity. [provided by RefSeq, Apr 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_004472.3.
BS2
High AC in GnomAd4 at 10 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXD1 | ENST00000615637.3 | c.1146_1160dupGCAGGCCGCCGCCGC | p.Ala387_Ala388insGlnAlaAlaAlaAla | disruptive_inframe_insertion | Exon 1 of 1 | 6 | NM_004472.3 | ENSP00000481581.1 | ||
FOXD1 | ENST00000513595.1 | n.-229_-215dupGCAGGCCGCCGCCGC | upstream_gene_variant | 3 | ||||||
FOXD1-AS1 | ENST00000514661.1 | n.*218_*219insGCGGCGGCGGCCTGC | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000686 AC: 10AN: 145856Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.000125 AC: 106AN: 846804Hom.: 0 Cov.: 30 AF XY: 0.000122 AC XY: 48AN XY: 393836
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GnomAD4 genome AF: 0.0000686 AC: 10AN: 145856Hom.: 0 Cov.: 32 AF XY: 0.0000423 AC XY: 3AN XY: 70912
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at