rs10234057
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000712.4(BLVRA):c.12+51C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 1,589,976 control chromosomes in the GnomAD database, including 30,046 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.15 ( 2208 hom., cov: 32)
Exomes 𝑓: 0.19 ( 27838 hom. )
Consequence
BLVRA
NM_000712.4 intron
NM_000712.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.262
Genes affected
BLVRA (HGNC:1062): (biliverdin reductase A) The protein encoded by this gene belongs to the biliverdin reductase family, members of which catalyze the conversion of biliverdin to bilirubin in the presence of NADPH or NADH. Mutations in this gene are associated with hyperbiliverdinemia. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BLVRA | NM_000712.4 | c.12+51C>T | intron_variant | ENST00000265523.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BLVRA | ENST00000265523.9 | c.12+51C>T | intron_variant | 1 | NM_000712.4 | P1 | |||
BLVRA | ENST00000402924.5 | c.12+51C>T | intron_variant | 2 | P1 | ||||
BLVRA | ENST00000424330.1 | c.12+51C>T | intron_variant | 3 | |||||
BLVRA | ENST00000453612.1 | n.36+51C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.152 AC: 23131AN: 152028Hom.: 2208 Cov.: 32
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GnomAD3 exomes AF: 0.158 AC: 39740AN: 250872Hom.: 3674 AF XY: 0.164 AC XY: 22283AN XY: 135574
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GnomAD4 exome AF: 0.190 AC: 273230AN: 1437830Hom.: 27838 Cov.: 29 AF XY: 0.189 AC XY: 135746AN XY: 716798
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GnomAD4 genome ? AF: 0.152 AC: 23126AN: 152146Hom.: 2208 Cov.: 32 AF XY: 0.149 AC XY: 11070AN XY: 74366
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at