13-52024762-T-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001004127.3(ALG11):c.1032T>G(p.Gly344Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000582 in 1,614,068 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001004127.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALG11 | NM_001004127.3 | c.1032T>G | p.Gly344Gly | synonymous_variant | Exon 3 of 4 | ENST00000521508.2 | NP_001004127.2 | |
UTP14C | NM_021645.6 | c.-662T>G | 5_prime_UTR_variant | Exon 1 of 2 | ENST00000521776.2 | NP_067677.4 | ||
ALG11 | NR_036571.3 | n.66-3557T>G | intron_variant | Intron 1 of 1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALG11 | ENST00000521508.2 | c.1032T>G | p.Gly344Gly | synonymous_variant | Exon 3 of 4 | 1 | NM_001004127.3 | ENSP00000430236.1 | ||
UTP14C | ENST00000521776 | c.-662T>G | 5_prime_UTR_variant | Exon 1 of 2 | 1 | NM_021645.6 | ENSP00000428619.1 |
Frequencies
GnomAD3 genomes AF: 0.00325 AC: 494AN: 152084Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000835 AC: 210AN: 251364Hom.: 1 AF XY: 0.000596 AC XY: 81AN XY: 135858
GnomAD4 exome AF: 0.000306 AC: 447AN: 1461866Hom.: 5 Cov.: 31 AF XY: 0.000287 AC XY: 209AN XY: 727234
GnomAD4 genome AF: 0.00324 AC: 493AN: 152202Hom.: 3 Cov.: 32 AF XY: 0.00317 AC XY: 236AN XY: 74420
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:1
- -
ALG11-congenital disorder of glycosylation Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at