chrX-13040783-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_174901.6(FAM9C):c.304G>A(p.Val102Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000152 in 1,185,242 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V102A) has been classified as Uncertain significance.
Frequency
Consequence
NM_174901.6 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 | UniProt |
---|---|---|---|---|---|---|---|
FAM9C | NM_174901.6 | c.304G>A | p.Val102Ile | missense_variant | 5/8 | ENST00000380625.8 | |
FAM9C | XM_024452348.2 | c.616G>A | p.Val206Ile | missense_variant | 5/7 | ||
FAM9C | XM_005274460.4 | c.304G>A | p.Val102Ile | missense_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM9C | ENST00000380625.8 | c.304G>A | p.Val102Ile | missense_variant | 5/8 | 1 | NM_174901.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000444 AC: 5AN: 112592Hom.: 0 Cov.: 24 AF XY: 0.0000863 AC XY: 3AN XY: 34754
GnomAD4 exome AF: 0.0000121 AC: 13AN: 1072650Hom.: 0 Cov.: 26 AF XY: 0.0000116 AC XY: 4AN XY: 345118
GnomAD4 genome AF: 0.0000444 AC: 5AN: 112592Hom.: 0 Cov.: 24 AF XY: 0.0000863 AC XY: 3AN XY: 34754
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2022 | The c.304G>A (p.V102I) alteration is located in exon 5 (coding exon 4) of the FAM9C gene. This alteration results from a G to A substitution at nucleotide position 304, causing the valine (V) at amino acid position 102 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