rs10233867

Positions:

• chr7-43767670-A-G

Variant summary

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

The NM_000712.4(BLVRA):​c.-21-3468A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 609,330 control chromosomes in the GnomAD database, including 10,114 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 0.14 (2157 hom., cov: 32)
  • Exomes 𝑓: 0.18 (7957 hom.)
• Consequence: BLVRA NM_000712.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

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=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLVRA	NM_000712.4	c.-21-3468A>G		intron_variant		ENST00000265523.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLVRA	ENST00000265523.9	c.-21-3468A>G		intron_variant		1	NM_000712.4	P1
BLVRA	ENST00000402924.5	c.-21-3468A>G		intron_variant		2		P1
BLVRA	ENST00000424330.1	c.-22+3365A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22052 AN: 152056 Hom.: 2157 Cov.: 32

Gnomad AFR AF: 0.0377

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.00788

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.147

GnomAD4 exome AF: 0.178 AC: 81336 AN: 457156 Hom.: 7957 AF XY: 0.178 AC XY: 44935 AN XY: 252672

Gnomad4 AFR exome AF: 0.0346

Gnomad4 AMR exome AF: 0.0998

Gnomad4 ASJ exome AF: 0.188

Gnomad4 EAS exome AF: 0.00572

Gnomad4 SAS exome AF: 0.127

Gnomad4 FIN exome AF: 0.220

Gnomad4 NFE exome AF: 0.213

Gnomad4 OTH exome AF: 0.174

GnomAD4 genome AF: 0.145 AC: 22043 AN: 152174 Hom.: 2157 Cov.: 32 AF XY: 0.142 AC XY: 10535 AN XY: 74376

Gnomad4 AFR AF: 0.0376

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.00790

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.145

Alfa AF: 0.181 Hom.: 403

Bravo AF: 0.132

Asia WGS AF: 0.0620 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	14
DANN	Benign	0.96

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: rs10233867; hg19: chr7-43807269;