3-172295420-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_022763.4(FNDC3B):āc.907T>Cā(p.Ser303Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,613,992 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_022763.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FNDC3B | NM_022763.4 | c.907T>C | p.Ser303Pro | missense_variant | 8/26 | ENST00000415807.7 | NP_073600.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FNDC3B | ENST00000415807.7 | c.907T>C | p.Ser303Pro | missense_variant | 8/26 | 1 | NM_022763.4 | ENSP00000411242.2 | ||
FNDC3B | ENST00000336824.8 | c.907T>C | p.Ser303Pro | missense_variant | 8/26 | 1 | ENSP00000338523.4 | |||
FNDC3B | ENST00000416957.5 | c.907T>C | p.Ser303Pro | missense_variant | 8/26 | 1 | ENSP00000389094.1 | |||
FNDC3B | ENST00000469491.5 | n.1048T>C | non_coding_transcript_exon_variant | 8/16 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152252Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251414Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135880
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461740Hom.: 0 Cov.: 30 AF XY: 0.0000151 AC XY: 11AN XY: 727192
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152252Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 21, 2024 | The c.907T>C (p.S303P) alteration is located in exon 8 (coding exon 7) of the FNDC3B gene. This alteration results from a T to C substitution at nucleotide position 907, causing the serine (S) at amino acid position 303 to be replaced by a proline (P). 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