chr11-119085172-CTTTTTTTTTTTT-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BS1
The NM_000190.4(HMBS):c.33+124_33+135del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00458 in 798,458 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00097 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0049 ( 1 hom. )
Consequence
HMBS
NM_000190.4 intron
NM_000190.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.83
Genes affected
HMBS (HGNC:4982): (hydroxymethylbilane synthase) This gene encodes a member of the hydroxymethylbilane synthase superfamily. The encoded protein is the third enzyme of the heme biosynthetic pathway and catalyzes the head to tail condensation of four porphobilinogen molecules into the linear hydroxymethylbilane. Mutations in this gene are associated with the autosomal dominant disease acute intermittent porphyria. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BS1
?
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.00491 (3593/731650) while in subpopulation AFR AF= 0.0105 (192/18268). AF 95% confidence interval is 0.00929. There are 1 homozygotes in gnomad4_exome. There are 1789 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HMBS | NM_000190.4 | c.33+124_33+135del | intron_variant | ENST00000652429.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HMBS | ENST00000652429.1 | c.33+124_33+135del | intron_variant | NM_000190.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.000973 AC: 65AN: 66772Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.00491 AC: 3593AN: 731650Hom.: 1 AF XY: 0.00494 AC XY: 1789AN XY: 361880
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at