rs2690381

chr7-43803185-C-T

Variant summary

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

The NM_000712.4(BLVRA):c.461-491C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,152 control chromosomes in the GnomAD database, including 5,514 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 0.24 (5514 hom., cov: 33)
• Consequence: BLVRA NM_000712.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLVRA	NM_000712.4	c.461-491C>T		intron_variant		ENST00000265523.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLVRA	ENST00000265523.9	c.461-491C>T		intron_variant		1	NM_000712.4	P1
BLVRA	ENST00000402924.5	c.461-491C>T		intron_variant		2		P1
BLVRA	ENST00000486984.1	n.165-491C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36869 AN: 152034 Hom.: 5516 Cov.: 33

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.242 AC: 36865 AN: 152152 Hom.: 5514 Cov.: 33 AF XY: 0.246 AC XY: 18284 AN XY: 74376

Gnomad4 AFR AF: 0.0579

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.265

Alfa AF: 0.277 Hom.: 1312

Bravo AF: 0.234

Asia WGS AF: 0.357 AC: 1240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.56
Dann	Benign	0.33

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: rs2690381; hg19: chr7-43842784;