X-9027885-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_205849.3(FAM9B):c.475C>T(p.Arg159Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000538 in 1,207,570 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 36 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R159H) has been classified as Uncertain significance.
Frequency
Consequence
NM_205849.3 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 |
---|---|---|---|---|---|---|---|
FAM9B | NM_205849.3 | c.475C>T | p.Arg159Cys | missense_variant | 7/9 | ENST00000327220.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM9B | ENST00000327220.10 | c.475C>T | p.Arg159Cys | missense_variant | 7/9 | 1 | NM_205849.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000536 AC: 6AN: 111860Hom.: 0 Cov.: 22 AF XY: 0.000117 AC XY: 4AN XY: 34058
GnomAD3 exomes AF: 0.0000928 AC: 17AN: 183182Hom.: 0 AF XY: 0.000163 AC XY: 11AN XY: 67680
GnomAD4 exome AF: 0.0000538 AC: 59AN: 1095657Hom.: 0 Cov.: 28 AF XY: 0.0000886 AC XY: 32AN XY: 361297
GnomAD4 genome AF: 0.0000536 AC: 6AN: 111913Hom.: 0 Cov.: 22 AF XY: 0.000117 AC XY: 4AN XY: 34121
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2023 | The c.475C>T (p.R159C) alteration is located in exon 6 (coding exon 6) of the FAM9B gene. This alteration results from a C to T substitution at nucleotide position 475, causing the arginine (R) at amino acid position 159 to be replaced by a cysteine (C). 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