chr9-113391611-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000031.6(ALAD):āc.177G>Cā(p.Lys59Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0833 in 1,613,738 control chromosomes in the GnomAD database, including 6,502 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_000031.6 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALAD | NM_000031.6 | c.177G>C | p.Lys59Asn | missense_variant | 4/12 | ENST00000409155.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALAD | ENST00000409155.8 | c.177G>C | p.Lys59Asn | missense_variant | 4/12 | 1 | NM_000031.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0627 AC: 9536AN: 152168Hom.: 417 Cov.: 32
GnomAD3 exomes AF: 0.0827 AC: 20774AN: 251162Hom.: 1166 AF XY: 0.0896 AC XY: 12168AN XY: 135792
GnomAD4 exome AF: 0.0855 AC: 124884AN: 1461452Hom.: 6086 Cov.: 32 AF XY: 0.0878 AC XY: 63842AN XY: 727058
GnomAD4 genome AF: 0.0626 AC: 9532AN: 152286Hom.: 416 Cov.: 32 AF XY: 0.0633 AC XY: 4716AN XY: 74466
ClinVar
Submissions by phenotype
Porphobilinogen synthase deficiency Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 05, 2022 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | This variant is associated with the following publications: (PMID: 25239657, 16909025, 9593628, 11342419, 11071662) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
AMINOLEVULINATE DEHYDRATASE, ALAD*1/ALAD*2 POLYMORPHISM Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 1991 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at