NM_000712.4:c.13-6050G>A

Variant names:

• chr7-43781854-G-A
• rs849161
• NM_000712.4:c.13-6050G>A

Variant summary

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

The NM_000712.4(BLVRA):​c.13-6050G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,908 control chromosomes in the GnomAD database, including 15,430 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 0.44 (15430 hom., cov: 31)
• Consequence: BLVRA NM_000712.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 9 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, AR, Unknown Classification: MODERATE, SUPPORTIVE, LIMITED Submitted by: Orphanet, ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLVRA	NM_000712.4	MANE Select	c.13-6050G>A		intron	N/A	NP_000703.2
	BLVRA	NM_001253823.2		c.13-6050G>A		intron	N/A	NP_001240752.1	A0A140VJF4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLVRA	ENST00000265523.9	TSL:1 MANE Select	c.13-6050G>A		intron	N/A	ENSP00000265523.4	P53004
	BLVRA	ENST00000940902.1		c.13-6050G>A		intron	N/A	ENSP00000610961.1
	BLVRA	ENST00000854107.1		c.13-6050G>A		intron	N/A	ENSP00000524166.1

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67190 AN: 151790 Hom.: 15419 Cov.: 31

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.443 AC: 67247 AN: 151908 Hom.: 15430 Cov.: 31 AF XY: 0.443 AC XY: 32903 AN XY: 74232

African (AFR) AF: 0.581 AC: 24030 AN: 41380

American (AMR) AF: 0.394 AC: 6019 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1638 AN: 3470

East Asian (EAS) AF: 0.418 AC: 2161 AN: 5170

South Asian (SAS) AF: 0.542 AC: 2603 AN: 4800

European-Finnish (FIN) AF: 0.383 AC: 4042 AN: 10550

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25349 AN: 67948

Other (OTH) AF: 0.430 AC: 905 AN: 2106

Alfa AF: 0.389 Hom.: 20162

Bravo AF: 0.447

Asia WGS AF: 0.475 AC: 1654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.4
DANN	Benign	0.59
PhyloP100		-0.23
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: rs849161; hg19: chr7-43821453;