7-43792704-G-A
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_000712.4(BLVRA):c.255-11G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,612,562 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000048 ( 0 hom. )
Consequence
BLVRA
NM_000712.4 splice_polypyrimidine_tract, intron
NM_000712.4 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.0007517
2
Clinical Significance
Conservation
PhyloP100: -0.287
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 Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 7-43792704-G-A is Benign according to our data. Variant chr7-43792704-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1987531.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BLVRA | NM_000712.4 | c.255-11G>A | splice_polypyrimidine_tract_variant, intron_variant | ENST00000265523.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BLVRA | ENST00000265523.9 | c.255-11G>A | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000712.4 | P1 | |||
BLVRA | ENST00000402924.5 | c.255-11G>A | splice_polypyrimidine_tract_variant, intron_variant | 2 | P1 | ||||
BLVRA | ENST00000424330.1 | c.255-11G>A | splice_polypyrimidine_tract_variant, intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152128Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000247 AC: 62AN: 251002Hom.: 0 AF XY: 0.000206 AC XY: 28AN XY: 135680
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GnomAD4 exome AF: 0.0000479 AC: 70AN: 1460316Hom.: 0 Cov.: 30 AF XY: 0.0000427 AC XY: 31AN XY: 726582
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GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74430
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 10, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at