X-8800093-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_174951.3(FAM9A):c.79G>T(p.Ala27Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000119 in 1,096,354 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/17 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM9A | NM_174951.3 | c.79G>T | p.Ala27Ser | missense_variant | 2/10 | ENST00000381003.7 | |
FAM9A | NM_001171186.1 | c.79G>T | p.Ala27Ser | missense_variant | 2/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM9A | ENST00000381003.7 | c.79G>T | p.Ala27Ser | missense_variant | 2/10 | 1 | NM_174951.3 | P1 | |
FAM9A | ENST00000543214.1 | c.79G>T | p.Ala27Ser | missense_variant | 2/10 | 1 | P1 |
Frequencies
GnomAD3 genomes Cov.: 20
GnomAD3 exomes AF: 0.0000165 AC: 3AN: 181980Hom.: 0 AF XY: 0.0000149 AC XY: 1AN XY: 67004
GnomAD4 exome AF: 0.0000119 AC: 13AN: 1096354Hom.: 0 Cov.: 30 AF XY: 0.00000829 AC XY: 3AN XY: 361846
GnomAD4 genome Cov.: 20
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 26, 2022 | The c.79G>T (p.A27S) alteration is located in exon 2 (coding exon 1) of the FAM9A gene. This alteration results from a G to T substitution at nucleotide position 79, causing the alanine (A) at amino acid position 27 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