chr11-78101102-G-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_024079.5(ALG8):āc.1443C>Gā(p.Thr481=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000756 in 1,614,068 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. T481T) has been classified as Likely benign.
Frequency
Consequence
NM_024079.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALG8 | NM_024079.5 | c.1443C>G | p.Thr481= | synonymous_variant | 13/13 | ENST00000299626.10 | |
ALG8 | XM_005274247.4 | c.1416C>G | p.Thr472= | synonymous_variant | 13/13 | ||
ALG8 | NM_001007027.3 | c.*114C>G | 3_prime_UTR_variant | 14/14 | |||
ALG8 | XR_950044.4 | n.1341C>G | non_coding_transcript_exon_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALG8 | ENST00000299626.10 | c.1443C>G | p.Thr481= | synonymous_variant | 13/13 | 1 | NM_024079.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000506 AC: 77AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000127 AC: 32AN: 251358Hom.: 1 AF XY: 0.0000736 AC XY: 10AN XY: 135832
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461874Hom.: 1 Cov.: 33 AF XY: 0.0000165 AC XY: 12AN XY: 727242
GnomAD4 genome AF: 0.000506 AC: 77AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.000699 AC XY: 52AN XY: 74374
ClinVar
Submissions by phenotype
ALG8 congenital disorder of glycosylation;C4693472:Polycystic liver disease 3 with or without kidney cysts Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 19, 2021 | - - |
ALG8 congenital disorder of glycosylation Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 26, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at