rs849165

chr7-43787815-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000712.4(BLVRA):c.13-89G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 1,604,566 control chromosomes in the GnomAD database, including 209,324 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 0.55 (23233 hom., cov: 31)
  • Exomes 𝑓: 0.50 (186091 hom.)
• Consequence: BLVRA NM_000712.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLVRA	NM_000712.4	c.13-89G>A		intron_variant		ENST00000265523.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLVRA	ENST00000265523.9	c.13-89G>A		intron_variant		1	NM_000712.4	P1
BLVRA	ENST00000402924.5	c.13-89G>A		intron_variant		2		P1
BLVRA	ENST00000424330.1	c.13-89G>A		intron_variant		3
BLVRA	ENST00000453612.1	n.37-89G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83390 AN: 151762 Hom.: 23201 Cov.: 31

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.545

GnomAD4 exome AF: 0.503 AC: 731397 AN: 1452686 Hom.: 186091 AF XY: 0.505 AC XY: 365518 AN XY: 723264

Gnomad4 AFR exome AF: 0.650

Gnomad4 AMR exome AF: 0.608

Gnomad4 ASJ exome AF: 0.559

Gnomad4 EAS exome AF: 0.452

Gnomad4 SAS exome AF: 0.599

Gnomad4 FIN exome AF: 0.519

Gnomad4 NFE exome AF: 0.486

Gnomad4 OTH exome AF: 0.523

GnomAD4 genome AF: 0.550 AC: 83479 AN: 151880 Hom.: 23233 Cov.: 31 AF XY: 0.552 AC XY: 41012 AN XY: 74230

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.547

Alfa AF: 0.507 Hom.: 26642

Bravo AF: 0.557

Asia WGS AF: 0.582 AC: 2025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.10
Dann	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs849165; hg19: chr7-43827414; COSMIC: COSV55515809;