rs4403725
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_145235.5(FANK1):c.14-26454A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,938 control chromosomes in the GnomAD database, including 11,639 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 0.39 ( 11639 hom., cov: 31)
Consequence
FANK1
NM_145235.5 intron
NM_145235.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.190
Genes affected
FANK1 (HGNC:23527): (fibronectin type III and ankyrin repeat domains 1) Involved in regulation of apoptotic process and regulation of transcription, DNA-templated. Located in cytosol and nucleoplasm. Colocalizes with chromatin. [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=-0.91).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANK1 | NM_145235.5 | c.14-26454A>G | intron_variant | ENST00000368693.6 | |||
FANK1 | NM_001350939.2 | c.14-26454A>G | intron_variant | ||||
FANK1 | NM_001363549.2 | c.-5-26454A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANK1 | ENST00000368693.6 | c.14-26454A>G | intron_variant | 1 | NM_145235.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.386 AC: 58571AN: 151820Hom.: 11624 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.386 AC: 58622AN: 151938Hom.: 11639 Cov.: 31 AF XY: 0.383 AC XY: 28450AN XY: 74242
GnomAD4 genome
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58622
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151938
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31
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28450
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74242
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Asia WGS
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1240
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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