chr3-46676321-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_147129.5(ALS2CL):c.2110G>A(p.Gly704Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000112 in 1,613,806 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_147129.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALS2CL | NM_147129.5 | c.2110G>A | p.Gly704Arg | missense_variant | Exon 19 of 26 | ENST00000318962.9 | NP_667340.2 | |
ALS2CL | NM_001190707.2 | c.2110G>A | p.Gly704Arg | missense_variant | Exon 19 of 26 | NP_001177636.1 | ||
ALS2CL | NR_033815.3 | n.2168G>A | non_coding_transcript_exon_variant | Exon 19 of 26 | ||||
ALS2CL | NR_135622.2 | n.2168G>A | non_coding_transcript_exon_variant | Exon 19 of 25 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000987 AC: 15AN: 152032Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000187 AC: 47AN: 251366Hom.: 0 AF XY: 0.000221 AC XY: 30AN XY: 135868
GnomAD4 exome AF: 0.000114 AC: 166AN: 1461656Hom.: 0 Cov.: 30 AF XY: 0.000162 AC XY: 118AN XY: 727158
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2110G>A (p.G704R) alteration is located in exon 19 (coding exon 18) of the ALS2CL gene. This alteration results from a G to A substitution at nucleotide position 2110, causing the glycine (G) at amino acid position 704 to be replaced by an arginine (R). 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