X-13043759-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_174901.6(FAM9C):c.31G>A(p.Val11Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000603 in 1,211,165 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 24 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_174901.6 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 |
---|---|---|---|---|---|---|---|
FAM9C | NM_174901.6 | c.31G>A | p.Val11Ile | missense_variant | 2/8 | ENST00000380625.8 | |
FAM9C | XM_024452348.2 | c.343G>A | p.Val115Ile | missense_variant | 2/7 | ||
FAM9C | XM_005274460.4 | c.31G>A | p.Val11Ile | missense_variant | 2/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM9C | ENST00000380625.8 | c.31G>A | p.Val11Ile | missense_variant | 2/8 | 1 | NM_174901.6 | P1 | |
FAM9C | ENST00000333995.7 | c.31G>A | p.Val11Ile | missense_variant | 2/7 | 1 | P1 | ||
FAM9C | ENST00000542843.5 | c.31G>A | p.Val11Ile | missense_variant | 2/6 | 1 | |||
FAM9C | ENST00000468287.1 | n.241G>A | non_coding_transcript_exon_variant | 2/7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000620 AC: 7AN: 112943Hom.: 0 Cov.: 24 AF XY: 0.0000570 AC XY: 2AN XY: 35069
GnomAD3 exomes AF: 0.0000382 AC: 7AN: 183413Hom.: 0 AF XY: 0.0000590 AC XY: 4AN XY: 67847
GnomAD4 exome AF: 0.0000601 AC: 66AN: 1098222Hom.: 0 Cov.: 30 AF XY: 0.0000605 AC XY: 22AN XY: 363576
GnomAD4 genome AF: 0.0000620 AC: 7AN: 112943Hom.: 0 Cov.: 24 AF XY: 0.0000570 AC XY: 2AN XY: 35069
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2024 | The c.31G>A (p.V11I) alteration is located in exon 2 (coding exon 1) of the FAM9C gene. This alteration results from a G to A substitution at nucleotide position 31, causing the valine (V) at amino acid position 11 to be replaced by an isoleucine (I). 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