rs601277
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022763.4(FNDC3B):c.2250+382A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,098 control chromosomes in the GnomAD database, including 17,305 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 0.45 ( 17305 hom., cov: 32)
Consequence
FNDC3B
NM_022763.4 intron
NM_022763.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0280
Genes affected
FNDC3B (HGNC:24670): (fibronectin type III domain containing 3B) Enables RNA binding activity. Predicted to act upstream of or within several processes, including negative regulation of osteoblast differentiation; substrate adhesion-dependent cell spreading; and type II pneumocyte differentiation. Predicted to be located in endoplasmic reticulum. [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=-0.84).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FNDC3B | NM_022763.4 | c.2250+382A>G | intron_variant | ENST00000415807.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FNDC3B | ENST00000415807.7 | c.2250+382A>G | intron_variant | 1 | NM_022763.4 | P1 | |||
FNDC3B | ENST00000336824.8 | c.2250+382A>G | intron_variant | 1 | P1 | ||||
FNDC3B | ENST00000416957.5 | c.2250+382A>G | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.446 AC: 67794AN: 151980Hom.: 17301 Cov.: 32
GnomAD3 genomes
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67794
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151980
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.446 AC: 67814AN: 152098Hom.: 17305 Cov.: 32 AF XY: 0.440 AC XY: 32710AN XY: 74334
GnomAD4 genome
?
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AC:
67814
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152098
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32
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32710
AN XY:
74334
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1202
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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