rs726344
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_153756.3(FNDC5):c.499+250C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,208 control chromosomes in the GnomAD database, including 2,372 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.16 ( 2372 hom., cov: 32)
Consequence
FNDC5
NM_153756.3 intron
NM_153756.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.895
Genes affected
FNDC5 (HGNC:20240): (fibronectin type III domain containing 5) This gene encodes a secreted protein that is released from muscle cells during exercise. The encoded protein may participate in the development of brown fat. Translation of the precursor protein initiates at a non-AUG start codon at a position that is conserved as an AUG start codon in other organisms. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 1-32867503-G-A is Benign according to our data. Variant chr1-32867503-G-A is described in ClinVar as [Benign]. Clinvar id is 1236585.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FNDC5 | NM_153756.3 | c.499+250C>T | intron_variant | ENST00000373471.9 | NP_715637.2 | |||
FNDC5 | NM_001171940.2 | c.499+250C>T | intron_variant | NP_001165411.2 | ||||
FNDC5 | NM_001171941.3 | c.274+250C>T | intron_variant | NP_001165412.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FNDC5 | ENST00000373471.9 | c.499+250C>T | intron_variant | 2 | NM_153756.3 | ENSP00000362570 | ||||
FNDC5 | ENST00000496770.1 | c.274+250C>T | intron_variant | 1 | ENSP00000476320 | |||||
FNDC5 | ENST00000649537.2 | c.466+250C>T | intron_variant | ENSP00000497837 | ||||||
FNDC5 | ENST00000710568.1 | c.643+250C>T | intron_variant | ENSP00000518350 | P1 |
Frequencies
GnomAD3 genomes AF: 0.157 AC: 23945AN: 152090Hom.: 2364 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.158 AC: 23999AN: 152208Hom.: 2372 Cov.: 32 AF XY: 0.157 AC XY: 11715AN XY: 74434
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207
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 18, 2020 | This variant is associated with the following publications: (PMID: 25427998) - |
Computational scores
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Name
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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