rs7970524
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The 12-95996374-T-C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 194,572 control chromosomes in the GnomAD database, including 4,175 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.20 ( 3321 hom., cov: 33)
Exomes 𝑓: 0.17 ( 854 hom. )
Consequence
HAL
NM_002108.4 upstream_gene
NM_002108.4 upstream_gene
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.144
Genes affected
HAL (HGNC:4806): (histidine ammonia-lyase) Histidine ammonia-lyase is a cytosolic enzyme catalyzing the first reaction in histidine catabolism, the nonoxidative deamination of L-histidine to trans-urocanic acid. Histidine ammonia-lyase defects cause histidinemia which is characterized by increased histidine and histamine and decreased urocanic acid in body fluids. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 12-95996374-T-C is Benign according to our data. Variant chr12-95996374-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 369030.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAL | NM_002108.4 | upstream_gene_variant | ENST00000261208.8 | ||||
HAL | NM_001258333.2 | upstream_gene_variant | |||||
HAL | NM_001258334.2 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAL | ENST00000261208.8 | upstream_gene_variant | 1 | NM_002108.4 | P1 | ||||
HAL | ENST00000538703.5 | upstream_gene_variant | 2 | ||||||
HAL | ENST00000541929.5 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.199 AC: 30334AN: 152098Hom.: 3321 Cov.: 33
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GnomAD4 exome AF: 0.174 AC: 7373AN: 42356Hom.: 854 Cov.: 0 AF XY: 0.168 AC XY: 3702AN XY: 21978
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GnomAD4 genome ? AF: 0.199 AC: 30335AN: 152216Hom.: 3321 Cov.: 33 AF XY: 0.192 AC XY: 14259AN XY: 74440
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Histidinemia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at