7-43799912-A-G

Variant names:

• chr7-43799912-A-G
• rs1317916
• NM_000712.4:c.353-553A>G

Variant summary

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

The NM_000712.4(BLVRA):​c.353-553A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,256 control chromosomes in the GnomAD database, including 53,378 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 (53378 hom., cov: 32)
• Consequence: BLVRA NM_000712.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLVRA	NM_000712.4	c.353-553A>G		intron_variant	Intron 5 of 7	ENST00000265523.9	NP_000703.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLVRA	ENST00000265523.9	c.353-553A>G		intron_variant	Intron 5 of 7	1	NM_000712.4	ENSP00000265523.4
BLVRA	ENST00000402924.5	c.353-553A>G		intron_variant	Intron 6 of 8	2		ENSP00000385757.1

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126749 AN: 152138 Hom.: 53309 Cov.: 32

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.833 AC: 126882 AN: 152256 Hom.: 53378 Cov.: 32 AF XY: 0.833 AC XY: 61996 AN XY: 74432

Gnomad4 AFR AF: 0.950

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.818

Alfa AF: 0.816 Hom.: 8965

Bravo AF: 0.841

Asia WGS AF: 0.771 AC: 2683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.6
DANN	Benign	0.74

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: rs1317916; hg19: chr7-43839511;