3-46670994-T-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_147129.5(ALS2CL):c.2852A>T(p.Glu951Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000958 in 1,461,708 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALS2CL | NM_147129.5 | c.2852A>T | p.Glu951Val | missense_variant | 26/26 | ENST00000318962.9 | |
ALS2CL | NM_001190707.2 | c.2852A>T | p.Glu951Val | missense_variant | 26/26 | ||
ALS2CL | NR_033815.3 | n.3200A>T | non_coding_transcript_exon_variant | 26/26 | |||
ALS2CL | NR_135622.2 | n.3788A>T | non_coding_transcript_exon_variant | 25/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALS2CL | ENST00000318962.9 | c.2852A>T | p.Glu951Val | missense_variant | 26/26 | 1 | NM_147129.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000800 AC: 2AN: 250144Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135282
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461708Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727158
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 08, 2023 | The c.2852A>T (p.E951V) alteration is located in exon 26 (coding exon 25) of the ALS2CL gene. This alteration results from a A to T substitution at nucleotide position 2852, causing the glutamic acid (E) at amino acid position 951 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