rs10234057

chr7-43771221-C-T

Variant summary

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

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
• 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]

ACMG classification

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: 23131 AN: 152028 Hom.: 2208 Cov.: 32

Gnomad AFR AF: 0.0626

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.00791

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.152

GnomAD3 exomes AF: 0.158 AC: 39740 AN: 250872 Hom.: 3674 AF XY: 0.164 AC XY: 22283 AN XY: 135574

Gnomad AFR exome AF: 0.0591

Gnomad AMR exome AF: 0.0924

Gnomad ASJ exome AF: 0.183

Gnomad EAS exome AF: 0.00887

Gnomad SAS exome AF: 0.127

Gnomad FIN exome AF: 0.226

Gnomad NFE exome AF: 0.209

Gnomad OTH exome AF: 0.182

GnomAD4 exome AF: 0.190 AC: 273230 AN: 1437830 Hom.: 27838 Cov.: 29 AF XY: 0.189 AC XY: 135746 AN XY: 716798

Gnomad4 AFR exome AF: 0.0560

Gnomad4 AMR exome AF: 0.0965

Gnomad4 ASJ exome AF: 0.182

Gnomad4 EAS exome AF: 0.00467

Gnomad4 SAS exome AF: 0.125

Gnomad4 FIN exome AF: 0.219

Gnomad4 NFE exome AF: 0.210

Gnomad4 OTH exome AF: 0.171

GnomAD4 genome AF: 0.152 AC: 23126 AN: 152146 Hom.: 2208 Cov.: 32 AF XY: 0.149 AC XY: 11070 AN XY: 74366

Gnomad4 AFR AF: 0.0625

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.00792

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.150

Alfa AF: 0.171 Hom.: 617

Bravo AF: 0.141

Asia WGS AF: 0.0640 AC: 223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.7
Dann	Benign	0.30

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: rs10234057; hg19: chr7-43810820;