chr2-201307533-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001127391.3(FLACC1):c.865A>G(p.Ile289Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000134 in 1,614,044 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001127391.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLACC1 | NM_001127391.3 | c.865A>G | p.Ile289Val | missense_variant | 11/15 | ENST00000392257.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLACC1 | ENST00000392257.8 | c.865A>G | p.Ile289Val | missense_variant | 11/15 | 1 | NM_001127391.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152256Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000159 AC: 40AN: 251404Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135880
GnomAD4 exome AF: 0.000134 AC: 196AN: 1461670Hom.: 0 Cov.: 30 AF XY: 0.000133 AC XY: 97AN XY: 727148
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152374Hom.: 1 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74514
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2022 | The c.865A>G (p.I289V) alteration is located in exon 11 (coding exon 10) of the ALS2CR12 gene. This alteration results from a A to G substitution at nucleotide position 865, causing the isoleucine (I) at amino acid position 289 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