chr12-34026298-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_032834.4(ALG10):c.805G>A(p.Val269Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000801 in 1,614,098 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_032834.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALG10 | NM_032834.4 | c.805G>A | p.Val269Ile | missense_variant | Exon 3 of 3 | ENST00000266483.7 | NP_116223.3 | |
ALG10 | XM_024449230.2 | c.625G>A | p.Val209Ile | missense_variant | Exon 3 of 3 | XP_024304998.1 | ||
ALG10 | XM_024449231.2 | c.625G>A | p.Val209Ile | missense_variant | Exon 3 of 3 | XP_024304999.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00433 AC: 659AN: 152152Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00110 AC: 276AN: 251370Hom.: 1 AF XY: 0.000692 AC XY: 94AN XY: 135856
GnomAD4 exome AF: 0.000433 AC: 633AN: 1461828Hom.: 3 Cov.: 31 AF XY: 0.000348 AC XY: 253AN XY: 727210
GnomAD4 genome AF: 0.00433 AC: 660AN: 152270Hom.: 4 Cov.: 32 AF XY: 0.00420 AC XY: 313AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at