chr9-20740322-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001375567.1(FOCAD):c.374A>G(p.Gln125Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000262 in 1,603,948 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001375567.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOCAD | NM_001375567.1 | c.374A>G | p.Gln125Arg | missense_variant | 5/44 | ENST00000338382.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOCAD | ENST00000338382.11 | c.374A>G | p.Gln125Arg | missense_variant | 5/44 | 5 | NM_001375567.1 | P1 | |
FOCAD | ENST00000380249.5 | c.374A>G | p.Gln125Arg | missense_variant | 7/46 | 1 | P1 | ||
FOCAD | ENST00000604103.1 | n.169A>G | non_coding_transcript_exon_variant | 2/5 | 4 | ||||
FOCAD | ENST00000605031.5 | n.150A>G | non_coding_transcript_exon_variant | 2/5 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152008Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250064Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135142
GnomAD4 exome AF: 0.0000269 AC: 39AN: 1451940Hom.: 0 Cov.: 27 AF XY: 0.0000249 AC XY: 18AN XY: 722940
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152008Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74246
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 28, 2022 | The c.374A>G (p.Q125R) alteration is located in exon 7 (coding exon 4) of the FOCAD gene. This alteration results from a A to G substitution at nucleotide position 374, causing the glutamine (Q) at amino acid position 125 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | This sequence change replaces glutamine, which is neutral and polar, with arginine, which is basic and polar, at codon 125 of the FOCAD protein (p.Gln125Arg). This variant is present in population databases (rs373907768, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with FOCAD-related conditions. ClinVar contains an entry for this variant (Variation ID: 2209723). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at