rs2613843

Positions:

• chr19-40463296-C-T

Variant summary

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

The NM_000713.3(BLVRB):​c.79+2314G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,100 control chromosomes in the GnomAD database, including 29,982 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 0.61 (29982 hom., cov: 32)
• Consequence: BLVRB NM_000713.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

Genes affected

BLVRB (HGNC:1063): (biliverdin reductase B) Enables biliverdin reductase (NAD(P)+) activity and riboflavin reductase (NADPH) activity. Involved in heme catabolic process. Located in cytosol; nucleoplasm; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLVRB	NM_000713.3	c.79+2314G>A		intron_variant		ENST00000263368.9	NP_000704.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BLVRB	ENST00000263368.9	c.79+2314G>A		intron_variant		1	NM_000713.3	ENSP00000263368.3

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92330 AN: 151980 Hom.: 29930 Cov.: 32

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.608 AC: 92437 AN: 152100 Hom.: 29982 Cov.: 32 AF XY: 0.598 AC XY: 44467 AN XY: 74334

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.520

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.581

Alfa AF: 0.563 Hom.: 15065

Bravo AF: 0.623

Asia WGS AF: 0.375 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.34

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: rs2613843; hg19: chr19-40969203;