rs1454985
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001277313.2(FMN1):c.1867+30783A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,146 control chromosomes in the GnomAD database, including 11,079 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 0.36 ( 11079 hom., cov: 33)
Consequence
FMN1
NM_001277313.2 intron
NM_001277313.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.431
Genes affected
FMN1 (HGNC:3768): (formin 1) This gene belongs to the formin homology family and encodes a protein that has a role in the formation of adherens junction and the polymerization of linear actin cables. The homologous gene in mouse is associated with limb deformity. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FMN1 | NM_001277313.2 | c.1867+30783A>G | intron_variant | ENST00000616417.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FMN1 | ENST00000616417.5 | c.1867+30783A>G | intron_variant | 5 | NM_001277313.2 | A2 | |||
FMN1 | ENST00000561249.5 | c.1867+30783A>G | intron_variant | 5 | A2 | ||||
FMN1 | ENST00000674090.1 | n.170-30062A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.365 AC: 55501AN: 152026Hom.: 11075 Cov.: 33
GnomAD3 genomes
?
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55501
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.365 AC: 55518AN: 152146Hom.: 11079 Cov.: 33 AF XY: 0.371 AC XY: 27579AN XY: 74362
GnomAD4 genome
?
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55518
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152146
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33
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27579
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74362
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886
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at