rs173683
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_033449.3(FCHSD1):c.577-384G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 152,034 control chromosomes in the GnomAD database, including 26,845 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 0.58 ( 26845 hom., cov: 33)
Consequence
FCHSD1
NM_033449.3 intron
NM_033449.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0980
Genes affected
FCHSD1 (HGNC:25463): (FCH and double SH3 domains 1) Predicted to enable lipid binding activity. Predicted to be involved in neuromuscular synaptic transmission and positive regulation of actin filament polymerization. Predicted to be located in cell projection and perikaryon. Predicted to be active in neuromuscular junction and recycling endosome. Predicted to colocalize with cuticular plate. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FCHSD1 | NM_033449.3 | c.577-384G>C | intron_variant | ENST00000435817.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCHSD1 | ENST00000435817.7 | c.577-384G>C | intron_variant | 1 | NM_033449.3 | P1 | |||
FCHSD1 | ENST00000519800.1 | c.571-384G>C | intron_variant | 2 | |||||
FCHSD1 | ENST00000522783.5 | c.571-384G>C | intron_variant | 5 | |||||
FCHSD1 | ENST00000522126.5 | c.349-384G>C | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.583 AC: 88570AN: 151916Hom.: 26811 Cov.: 33
GnomAD3 genomes
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88570
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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: 0.583 AC: 88661AN: 152034Hom.: 26845 Cov.: 33 AF XY: 0.579 AC XY: 43028AN XY: 74324
GnomAD4 genome
?
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88661
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33
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43028
AN XY:
74324
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1520
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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
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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