chr12-29297064-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001271783.2(FAR2):c.409C>G(p.Leu137Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000391 in 1,612,220 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 (★).
Frequency
Consequence
NM_001271783.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAR2 | NM_001271783.2 | c.409C>G | p.Leu137Val | missense_variant | 4/12 | ENST00000536681.8 | |
LOC100506606 | NR_103860.1 | n.470-3524G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAR2 | ENST00000536681.8 | c.409C>G | p.Leu137Val | missense_variant | 4/12 | 1 | NM_001271783.2 | P1 | |
ENST00000553105.1 | n.470-3524G>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000602 AC: 15AN: 249048Hom.: 0 AF XY: 0.0000966 AC XY: 13AN XY: 134604
GnomAD4 exome AF: 0.0000384 AC: 56AN: 1459894Hom.: 0 Cov.: 31 AF XY: 0.0000386 AC XY: 28AN XY: 726158
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2023 | The c.409C>G (p.L137V) alteration is located in exon 4 (coding exon 3) of the FAR2 gene. This alteration results from a C to G substitution at nucleotide position 409, causing the leucine (L) at amino acid position 137 to be replaced by a valine (V). 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