rs806213
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020369.3(FSCN3):c.145-371C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000173 in 467,206 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00024 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00014 ( 0 hom. )
Consequence
FSCN3
NM_020369.3 intron
NM_020369.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.719
Genes affected
FSCN3 (HGNC:3961): (fascin actin-bundling protein 3) Predicted to enable actin filament binding activity. Predicted to be involved in actin filament bundle assembly; cell migration; and establishment or maintenance of cell polarity. Predicted to be located in cytoskeleton. Predicted to be active in several cellular components, including lamellipodium; microvillus; and ruffle. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FSCN3 | NM_020369.3 | c.145-371C>A | intron_variant | ENST00000265825.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FSCN3 | ENST00000265825.6 | c.145-371C>A | intron_variant | 1 | NM_020369.3 | P1 | |||
FSCN3 | ENST00000478328.1 | n.544-371C>A | intron_variant, non_coding_transcript_variant | 1 | |||||
FSCN3 | ENST00000478821.1 | c.-258-371C>A | intron_variant | 5 | |||||
FSCN3 | ENST00000421705.1 | c.*142C>A | 3_prime_UTR_variant, NMD_transcript_variant | 3/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000237 AC: 36AN: 152134Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.000143 AC: 45AN: 314954Hom.: 0 Cov.: 0 AF XY: 0.000130 AC XY: 23AN XY: 176390
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GnomAD4 genome ? AF: 0.000236 AC: 36AN: 152252Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74428
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ClinVar
Not reported inComputational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at