9-108939197-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_017832.4(ABITRAM):c.263G>A(p.Gly88Glu) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,612,894 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017832.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABITRAM | NM_017832.4 | c.263G>A | p.Gly88Glu | missense_variant, splice_region_variant | 4/6 | ENST00000322940.11 | |
ABITRAM | NM_001410990.1 | c.261+2760G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABITRAM | ENST00000322940.11 | c.263G>A | p.Gly88Glu | missense_variant, splice_region_variant | 4/6 | 1 | NM_017832.4 | P1 | |
ABITRAM | ENST00000445175.1 | c.158G>A | p.Gly53Glu | missense_variant, splice_region_variant | 3/5 | 3 | |||
ABITRAM | ENST00000374624.7 | c.261+2760G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250648Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135542
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460814Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726796
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74280
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2023 | The c.263G>A (p.G88E) alteration is located in exon 4 (coding exon 4) of the FAM206A gene. This alteration results from a G to A substitution at nucleotide position 263, causing the glycine (G) at amino acid position 88 to be replaced by a glutamic acid (E). 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