rs10486752

chr7-43762384-A-Gchr7-43762384-A-T

Variant summary

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

The NM_000712.4(BLVRA):c.-22+3650A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 151,742 control chromosomes in the GnomAD database, including 1,543 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 0.14 (1543 hom., cov: 30)
• Consequence: BLVRA NM_000712.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) 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.-22+3650A>G		intron_variant		ENST00000265523.9
BLVRA	NM_001253823.2	c.-22+2274A>G		intron_variant
BLVRA	XM_011515474.3	c.-22+4168A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLVRA	ENST00000265523.9	c.-22+3650A>G		intron_variant		1	NM_000712.4	P1
BLVRA	ENST00000402924.5	c.-22+2274A>G		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20902 AN: 151624 Hom.: 1537 Cov.: 30

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.145

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.138 AC: 20936 AN: 151742 Hom.: 1543 Cov.: 30 AF XY: 0.141 AC XY: 10453 AN XY: 74096

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.145

Alfa AF: 0.132 Hom.: 1874

Bravo AF: 0.134

Asia WGS AF: 0.185 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.2
Dann	Benign	0.67

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: rs10486752; hg19: chr7-43801983;