chrX-8799050-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_174951.3(FAM9A):c.136C>T(p.Pro46Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000553 in 1,211,109 control chromosomes in the GnomAD database, including 1 homozygotes. There are 22 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM9A | NM_174951.3 | c.136C>T | p.Pro46Ser | missense_variant | 3/10 | ENST00000381003.7 | |
FAM9A | NM_001171186.1 | c.136C>T | p.Pro46Ser | missense_variant | 3/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM9A | ENST00000381003.7 | c.136C>T | p.Pro46Ser | missense_variant | 3/10 | 1 | NM_174951.3 | P1 | |
FAM9A | ENST00000543214.1 | c.136C>T | p.Pro46Ser | missense_variant | 3/10 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000883 AC: 1AN: 113224Hom.: 0 Cov.: 24 AF XY: 0.0000283 AC XY: 1AN XY: 35382
GnomAD3 exomes AF: 0.0000110 AC: 2AN: 182339Hom.: 0 AF XY: 0.0000299 AC XY: 2AN XY: 66911
GnomAD4 exome AF: 0.0000601 AC: 66AN: 1097885Hom.: 1 Cov.: 31 AF XY: 0.0000578 AC XY: 21AN XY: 363261
GnomAD4 genome AF: 0.00000883 AC: 1AN: 113224Hom.: 0 Cov.: 24 AF XY: 0.0000283 AC XY: 1AN XY: 35382
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 14, 2023 | The c.136C>T (p.P46S) alteration is located in exon 3 (coding exon 2) of the FAM9A gene. This alteration results from a C to T substitution at nucleotide position 136, causing the proline (P) at amino acid position 46 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