7-43792717-A-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000712.4(BLVRA):c.257A>C(p.Gln86Pro) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Consequence
BLVRA
NM_000712.4 missense, splice_region
NM_000712.4 missense, splice_region
Scores
9
9
Clinical Significance
Conservation
PhyloP100: 3.28
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 Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BLVRA | NM_000712.4 | c.257A>C | p.Gln86Pro | missense_variant, splice_region_variant | 5/8 | ENST00000265523.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BLVRA | ENST00000265523.9 | c.257A>C | p.Gln86Pro | missense_variant, splice_region_variant | 5/8 | 1 | NM_000712.4 | P1 | |
BLVRA | ENST00000402924.5 | c.257A>C | p.Gln86Pro | missense_variant, splice_region_variant | 6/9 | 2 | P1 | ||
BLVRA | ENST00000424330.1 | c.257A>C | p.Gln86Pro | missense_variant, splice_region_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | The c.257A>C (p.Q86P) alteration is located in exon 5 (coding exon 4) of the BLVRA gene. This alteration results from a A to C substitution at nucleotide position 257, causing the glutamine (Q) at amino acid position 86 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;D
REVEL
Uncertain
Sift
Benign
T;T;D
Sift4G
Benign
T;T;T
Polyphen
D;D;.
Vest4
MutPred
Gain of catalytic residue at Q86 (P = 0.0435);Gain of catalytic residue at Q86 (P = 0.0435);Gain of catalytic residue at Q86 (P = 0.0435);
MVP
MPC
0.67
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.