chrX-8799056-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_174951.3(FAM9A):āc.130A>Gā(p.Met44Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000638 in 1,097,724 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. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_174951.3 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 |
---|---|---|---|---|---|---|---|
FAM9A | NM_174951.3 | c.130A>G | p.Met44Val | missense_variant | 3/10 | ENST00000381003.7 | |
FAM9A | NM_001171186.1 | c.130A>G | p.Met44Val | missense_variant | 3/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM9A | ENST00000381003.7 | c.130A>G | p.Met44Val | missense_variant | 3/10 | 1 | NM_174951.3 | P1 | |
FAM9A | ENST00000543214.1 | c.130A>G | p.Met44Val | missense_variant | 3/10 | 1 | P1 |
Frequencies
GnomAD3 genomes Cov.: 25
GnomAD3 exomes AF: 0.00000551 AC: 1AN: 181574Hom.: 0 AF XY: 0.0000151 AC XY: 1AN XY: 66204
GnomAD4 exome AF: 0.00000638 AC: 7AN: 1097724Hom.: 0 Cov.: 31 AF XY: 0.00000826 AC XY: 3AN XY: 363108
GnomAD4 genome Cov.: 25
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 04, 2024 | The c.130A>G (p.M44V) alteration is located in exon 3 (coding exon 2) of the FAM9A gene. This alteration results from a A to G substitution at nucleotide position 130, causing the methionine (M) at amino acid position 44 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