7-43799912-A-G

Variant names:

• chr7-43799912-A-G
• rs1317916
• NM_000712.4:c.353-553A>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.353-553A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,256 control chromosomes in the GnomAD database, including 53,378 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 (53378 hom., cov: 32)
• Consequence: BLVRA NM_000712.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.943 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.353-553A>G		intron	N/A	NP_000703.2
	BLVRA	NM_001253823.2		c.353-553A>G		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.353-553A>G		intron	N/A	ENSP00000265523.4	P53004
	BLVRA	ENST00000940902.1		c.386-553A>G		intron	N/A	ENSP00000610961.1
	BLVRA	ENST00000854107.1		c.353-553A>G		intron	N/A	ENSP00000524166.1

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126749 AN: 152138 Hom.: 53309 Cov.: 32

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.833 AC: 126882 AN: 152256 Hom.: 53378 Cov.: 32 AF XY: 0.833 AC XY: 61996 AN XY: 74432

African (AFR) AF: 0.950 AC: 39518 AN: 41582

American (AMR) AF: 0.861 AC: 13175 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2758 AN: 3470

East Asian (EAS) AF: 0.679 AC: 3519 AN: 5182

South Asian (SAS) AF: 0.832 AC: 4016 AN: 4828

European-Finnish (FIN) AF: 0.804 AC: 8517 AN: 10596

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.775 AC: 52676 AN: 67984

Other (OTH) AF: 0.818 AC: 1728 AN: 2112

Alfa AF: 0.797 Hom.: 73841

Bravo AF: 0.841

Asia WGS AF: 0.771 AC: 2683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.6
DANN	Benign	0.74
PhyloP100		0.13
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: rs1317916; hg19: chr7-43839511;