7-43782253-A-G

Variant names:

• chr7-43782253-A-G
• rs849162
• NM_000712.4:c.13-5651A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000712.4(BLVRA):​c.13-5651A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,158 control chromosomes in the GnomAD database, including 52,410 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 0.83 (52410 hom., cov: 32)
• Consequence: BLVRA NM_000712.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• 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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLVRA	NM_000712.4	c.13-5651A>G		intron_variant	Intron 2 of 7	ENST00000265523.9	NP_000703.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLVRA	ENST00000265523.9	c.13-5651A>G		intron_variant	Intron 2 of 7	1	NM_000712.4	ENSP00000265523.4
BLVRA	ENST00000402924.5	c.13-5651A>G		intron_variant	Intron 3 of 8	2		ENSP00000385757.1
BLVRA	ENST00000424330.1	c.13-5651A>G		intron_variant	Intron 2 of 4	3		ENSP00000412005.1
BLVRA	ENST00000453612.1	n.37-5651A>G		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125631 AN: 152040 Hom.: 52344 Cov.: 32

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.827 AC: 125763 AN: 152158 Hom.: 52410 Cov.: 32 AF XY: 0.826 AC XY: 61473 AN XY: 74382

African (AFR) AF: 0.935 AC: 38828 AN: 41518

American (AMR) AF: 0.858 AC: 13111 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2749 AN: 3470

East Asian (EAS) AF: 0.691 AC: 3570 AN: 5168

South Asian (SAS) AF: 0.831 AC: 4009 AN: 4826

European-Finnish (FIN) AF: 0.803 AC: 8499 AN: 10580

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52321 AN: 67988

Other (OTH) AF: 0.812 AC: 1717 AN: 2114

Alfa AF: 0.850 Hom.: 14926

Bravo AF: 0.834

Asia WGS AF: 0.775 AC: 2695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	9.3
DANN	Benign	0.93
PhyloP100		0.28
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: rs849162; hg19: chr7-43821852;