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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.257
Variant links:
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]
FOXD1-AS1 (HGNC:50658): (FOXD1 antisense RNA 1)

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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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FOXD1NM_004472.3 linkc.1146_1160dupGCAGGCCGCCGCCGC p.Ala387_Ala388insGlnAlaAlaAlaAla disruptive_inframe_insertion Exon 1 of 1 ENST00000615637.3 NP_004463.1 Q16676

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FOXD1ENST00000615637.3 linkc.1146_1160dupGCAGGCCGCCGCCGC p.Ala387_Ala388insGlnAlaAlaAlaAla disruptive_inframe_insertion Exon 1 of 1 6 NM_004472.3 ENSP00000481581.1 Q16676
FOXD1ENST00000513595.1 linkn.-229_-215dupGCAGGCCGCCGCCGC upstream_gene_variant 3
FOXD1-AS1ENST00000514661.1 linkn.*218_*219insGCGGCGGCGGCCTGC downstream_gene_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0000686
AC:
10
AN:
145856
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000152
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.000125
AC:
106
AN:
846804
Hom.:
0
Cov.:
30
AF XY:
0.000122
AC XY:
48
AN XY:
393836
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000743
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000131
Gnomad4 OTH exome
AF:
0.000143
GnomAD4 genome
AF:
0.0000686
AC:
10
AN:
145856
Hom.:
0
Cov.:
32
AF XY:
0.0000423
AC XY:
3
AN XY:
70912
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000152
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs771204220; hg19: chr5-72743029; API