chr3-172251521-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_022763.4(FNDC3B):c.770C>T(p.Ser257Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000614 in 1,612,868 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S257S) has been classified as Benign.
Frequency
Consequence
NM_022763.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FNDC3B | NM_022763.4 | c.770C>T | p.Ser257Leu | missense_variant | 6/26 | ENST00000415807.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FNDC3B | ENST00000415807.7 | c.770C>T | p.Ser257Leu | missense_variant | 6/26 | 1 | NM_022763.4 | P1 | |
FNDC3B | ENST00000336824.8 | c.770C>T | p.Ser257Leu | missense_variant | 6/26 | 1 | P1 | ||
FNDC3B | ENST00000416957.5 | c.770C>T | p.Ser257Leu | missense_variant | 6/26 | 1 | P1 | ||
FNDC3B | ENST00000469491.5 | n.911C>T | non_coding_transcript_exon_variant | 6/16 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152078Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000520 AC: 13AN: 250118Hom.: 0 AF XY: 0.0000740 AC XY: 10AN XY: 135224
GnomAD4 exome AF: 0.0000637 AC: 93AN: 1460672Hom.: 1 Cov.: 32 AF XY: 0.0000702 AC XY: 51AN XY: 726538
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152196Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74422
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2022 | The c.770C>T (p.S257L) alteration is located in exon 6 (coding exon 5) of the FNDC3B gene. This alteration results from a C to T substitution at nucleotide position 770, causing the serine (S) at amino acid position 257 to be replaced by a leucine (L). 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