chr7-43782253-A-G

Position:

• chr7-43782253-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.13-5651A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,158 control chromosomes in the GnomAD database, including 52,410 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 (52410 hom., cov: 32)
• Consequence: BLVRA NM_000712.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

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=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLVRA	NM_000712.4	c.13-5651A>G		intron_variant		ENST00000265523.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLVRA	ENST00000265523.9	c.13-5651A>G		intron_variant		1	NM_000712.4	P1
BLVRA	ENST00000402924.5	c.13-5651A>G		intron_variant		2		P1
BLVRA	ENST00000424330.1	c.13-5651A>G		intron_variant		3
BLVRA	ENST00000453612.1	n.37-5651A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125631 AN: 152040 Hom.: 52344 Cov.: 32

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.827 AC: 125763 AN: 152158 Hom.: 52410 Cov.: 32 AF XY: 0.826 AC XY: 61473 AN XY: 74382

Gnomad4 AFR AF: 0.935

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.831

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.812

Alfa AF: 0.813 Hom.: 8761

Bravo AF: 0.834

Asia WGS AF: 0.775 AC: 2695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	9.3
DANN	Benign	0.93

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: rs849162; hg19: chr7-43821852;