chr2-201330806-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001127391.3(FLACC1):c.552A>C(p.Glu184Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 1,613,678 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 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.552A>C | p.Glu184Asp | missense_variant | 8/15 | ENST00000392257.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLACC1 | ENST00000392257.8 | c.552A>C | p.Glu184Asp | missense_variant | 8/15 | 1 | NM_001127391.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152156Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000638 AC: 16AN: 250588Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135446
GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461404Hom.: 1 Cov.: 31 AF XY: 0.0000316 AC XY: 23AN XY: 726986
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152274Hom.: 0 Cov.: 31 AF XY: 0.0000537 AC XY: 4AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | The c.552A>C (p.E184D) alteration is located in exon 8 (coding exon 7) of the ALS2CR12 gene. This alteration results from a A to C substitution at nucleotide position 552, causing the glutamic acid (E) at amino acid position 184 to be replaced by an aspartic acid (D). 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