chr11-47743354-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_015308.5(FNBP4):c.1456+599C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0196 in 152,122 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.020 ( 37 hom., cov: 32)
Consequence
FNBP4
NM_015308.5 intron
NM_015308.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.616
Publications
1 publications found
Genes affected
FNBP4 (HGNC:19752): (formin binding protein 4) This gene encodes a protein containing two tryptophan-rich WW domains that binds the proline-rich formin homology 1 domains of formin family proteins, suggesting a role in the regulation of cytoskeletal dynamics during cell division and migration. It also binds intersectin family proteins suggesting a role in the maintenance of membrane curvature at sites of nascent vesicle formation. Naturally occurring mutations in this gene are associated with Waardenburg anophthalmia syndrome. [provided by RefSeq, Apr 2017]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0196 (2986/152122) while in subpopulation AFR AF = 0.0294 (1221/41508). AF 95% confidence interval is 0.028. There are 37 homozygotes in GnomAd4. There are 1386 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
BS2
High AC in GnomAd4 at 2986 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FNBP4 | ENST00000263773.10 | c.1456+599C>T | intron_variant | Intron 8 of 16 | 1 | NM_015308.5 | ENSP00000263773.5 | |||
FNBP4 | ENST00000527894.1 | n.191+599C>T | intron_variant | Intron 1 of 3 | 3 | |||||
FNBP4 | ENST00000528388.5 | n.63+599C>T | intron_variant | Intron 1 of 4 | 2 | |||||
FNBP4 | ENST00000534003.5 | n.1454+599C>T | intron_variant | Intron 8 of 10 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0196 AC: 2984AN: 152004Hom.: 37 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
2984
AN:
152004
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0196 AC: 2986AN: 152122Hom.: 37 Cov.: 32 AF XY: 0.0186 AC XY: 1386AN XY: 74384 show subpopulations
GnomAD4 genome
AF:
AC:
2986
AN:
152122
Hom.:
Cov.:
32
AF XY:
AC XY:
1386
AN XY:
74384
show subpopulations
African (AFR)
AF:
AC:
1221
AN:
41508
American (AMR)
AF:
AC:
331
AN:
15248
Ashkenazi Jewish (ASJ)
AF:
AC:
119
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5166
South Asian (SAS)
AF:
AC:
22
AN:
4814
European-Finnish (FIN)
AF:
AC:
65
AN:
10604
Middle Eastern (MID)
AF:
AC:
8
AN:
294
European-Non Finnish (NFE)
AF:
AC:
1172
AN:
67992
Other (OTH)
AF:
AC:
47
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
151
302
453
604
755
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
38
76
114
152
190
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
24
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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