NM_175736.5:c.127-3710C>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_175736.5(FMNL3):c.127-3710C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0812 in 152,000 control chromosomes in the GnomAD database, including 533 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 0.081 ( 533 hom., cov: 32)
Consequence
FMNL3
NM_175736.5 intron
NM_175736.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.81
Publications
6 publications found
Genes affected
FMNL3 (HGNC:23698): (formin like 3) The protein encoded by this gene contains a formin homology 2 domain and has high sequence identity to the mouse Wbp3 protein. Two alternative transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0912 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FMNL3 | ENST00000335154.10 | c.127-3710C>T | intron_variant | Intron 1 of 25 | 1 | NM_175736.5 | ENSP00000335655.5 | |||
FMNL3 | ENST00000550488.5 | c.127-3710C>T | intron_variant | Intron 1 of 26 | 5 | ENSP00000447479.1 | ||||
FMNL3 | ENST00000352151.9 | c.127-3710C>T | intron_variant | Intron 1 of 24 | 2 | ENSP00000344311.5 | ||||
FMNL3 | ENST00000550424.1 | c.34-3710C>T | intron_variant | Intron 2 of 3 | 4 | ENSP00000448939.1 |
Frequencies
GnomAD3 genomes AF: 0.0812 AC: 12332AN: 151882Hom.: 532 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
12332
AN:
151882
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: 0.0812 AC: 12345AN: 152000Hom.: 533 Cov.: 32 AF XY: 0.0783 AC XY: 5817AN XY: 74296 show subpopulations
GnomAD4 genome
AF:
AC:
12345
AN:
152000
Hom.:
Cov.:
32
AF XY:
AC XY:
5817
AN XY:
74296
show subpopulations
African (AFR)
AF:
AC:
3383
AN:
41434
American (AMR)
AF:
AC:
995
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
AC:
346
AN:
3470
East Asian (EAS)
AF:
AC:
141
AN:
5156
South Asian (SAS)
AF:
AC:
396
AN:
4808
European-Finnish (FIN)
AF:
AC:
467
AN:
10554
Middle Eastern (MID)
AF:
AC:
41
AN:
294
European-Non Finnish (NFE)
AF:
AC:
6332
AN:
67982
Other (OTH)
AF:
AC:
184
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
586
1172
1759
2345
2931
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
278
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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