rs10486752

Variant names:

• chr7-43762384-A-G
• rs10486752
• NM_000712.4:c.-22+3650A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-43762384-A-G
• chr7-43762384-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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]

BLVRA Gene-Disease associations (from GenCC):

• hyperbiliverdinemia

  Inheritance: AD, Unknown Classification: SUPPORTIVE, LIMITED Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics

LOC107986727 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000712.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLVRA	NM_000712.4	MANE Select	c.-22+3650A>G		intron	N/A	NP_000703.2
	BLVRA	NM_001253823.2		c.-22+2274A>G		intron	N/A	NP_001240752.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLVRA	ENST00000265523.9	TSL:1 MANE Select	c.-22+3650A>G		intron	N/A	ENSP00000265523.4
	BLVRA	ENST00000402924.5	TSL:2	c.-22+2274A>G		intron	N/A	ENSP00000385757.1

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

African (AFR) AF: 0.114 AC: 4721 AN: 41430

American (AMR) AF: 0.172 AC: 2612 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 556 AN: 3462

East Asian (EAS) AF: 0.221 AC: 1123 AN: 5070

South Asian (SAS) AF: 0.198 AC: 945 AN: 4784

European-Finnish (FIN) AF: 0.153 AC: 1609 AN: 10506

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8834 AN: 67954

Other (OTH) AF: 0.145 AC: 305 AN: 2108

Alfa AF: 0.133 Hom.: 2543

Bravo AF: 0.134

Asia WGS AF: 0.185 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.67
PhyloP100		0.035
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10486752; hg19: chr7-43801983;