chr3-172335071-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_022763.4(FNDC3B):āc.1769G>Cā(p.Ser590Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000562 in 1,600,040 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_022763.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FNDC3B | NM_022763.4 | c.1769G>C | p.Ser590Thr | missense_variant | 15/26 | ENST00000415807.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FNDC3B | ENST00000415807.7 | c.1769G>C | p.Ser590Thr | missense_variant | 15/26 | 1 | NM_022763.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000398 AC: 6AN: 150746Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000458 AC: 11AN: 240134Hom.: 0 AF XY: 0.0000384 AC XY: 5AN XY: 130106
GnomAD4 exome AF: 0.0000580 AC: 84AN: 1449228Hom.: 0 Cov.: 31 AF XY: 0.0000624 AC XY: 45AN XY: 720790
GnomAD4 genome AF: 0.0000398 AC: 6AN: 150812Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73512
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | The c.1769G>C (p.S590T) alteration is located in exon 15 (coding exon 14) of the FNDC3B gene. This alteration results from a G to C substitution at nucleotide position 1769, causing the serine (S) at amino acid position 590 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at