X-8798991-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_174951.3(FAM9A):c.195G>T(p.Arg65Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000182 in 1,098,229 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_174951.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM9A | NM_174951.3 | c.195G>T | p.Arg65Ser | missense_variant | 3/10 | ENST00000381003.7 | |
FAM9A | NM_001171186.1 | c.195G>T | p.Arg65Ser | missense_variant | 3/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM9A | ENST00000381003.7 | c.195G>T | p.Arg65Ser | missense_variant | 3/10 | 1 | NM_174951.3 | P1 | |
FAM9A | ENST00000543214.1 | c.195G>T | p.Arg65Ser | missense_variant | 3/10 | 1 | P1 |
Frequencies
GnomAD3 genomes Cov.: 25
GnomAD3 exomes AF: 0.00000546 AC: 1AN: 183307Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67761
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1098229Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 1AN XY: 363593
GnomAD4 genome Cov.: 25
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 25, 2022 | The c.195G>T (p.R65S) alteration is located in exon 3 (coding exon 2) of the FAM9A gene. This alteration results from a G to T substitution at nucleotide position 195, causing the arginine (R) at amino acid position 65 to be replaced by a serine (S). 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