rs849161

chr7-43781854-G-Achr7-43781854-G-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLVRA	NM_000712.4	c.13-6050G>A		intron_variant		ENST00000265523.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLVRA	ENST00000265523.9	c.13-6050G>A		intron_variant		1	NM_000712.4	P1
BLVRA	ENST00000402924.5	c.13-6050G>A		intron_variant		2		P1
BLVRA	ENST00000424330.1	c.13-6050G>A		intron_variant		3
BLVRA	ENST00000453612.1	n.37-6050G>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.430

Alfa AF: 0.382 Hom.: 15298

Bravo AF: 0.447

Asia WGS AF: 0.475 AC: 1654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.4
Dann	Benign	0.59

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: rs849161; hg19: chr7-43821453;