rs570549
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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.1971+100G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 861,140 control chromosomes in the GnomAD database, including 205,040 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 0.64 ( 32295 hom., cov: 33)
Exomes 𝑓: 0.69 ( 172745 hom. )
Consequence
FNDC3B
NM_022763.4 intron
NM_022763.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.866
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=-0.85).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FNDC3B | NM_022763.4 | c.1971+100G>A | intron_variant | ENST00000415807.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FNDC3B | ENST00000415807.7 | c.1971+100G>A | intron_variant | 1 | NM_022763.4 | P1 | |||
FNDC3B | ENST00000336824.8 | c.1971+100G>A | intron_variant | 1 | P1 | ||||
FNDC3B | ENST00000416957.5 | c.1971+100G>A | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.642 AC: 97541AN: 151974Hom.: 32271 Cov.: 33
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GnomAD4 exome AF: 0.695 AC: 492774AN: 709048Hom.: 172745 AF XY: 0.691 AC XY: 261933AN XY: 378978
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GnomAD4 genome ? AF: 0.642 AC: 97598AN: 152092Hom.: 32295 Cov.: 33 AF XY: 0.643 AC XY: 47805AN XY: 74340
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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