7-43787922-G-T

Variant names:

• chr7-43787922-G-T
• rs201359042
• NM_000712.4:c.31G>T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_000712.4(BLVRA):​c.31G>T​(p.Val11Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BLVRA NM_000712.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLVRA	NM_000712.4	c.31G>T	p.Val11Leu	missense_variant	Exon 3 of 8	ENST00000265523.9	NP_000703.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLVRA	ENST00000265523.9	c.31G>T	p.Val11Leu	missense_variant	Exon 3 of 8	1	NM_000712.4	ENSP00000265523.4
BLVRA	ENST00000402924.5	c.31G>T	p.Val11Leu	missense_variant	Exon 4 of 9	2		ENSP00000385757.1
BLVRA	ENST00000424330.1	c.31G>T	p.Val11Leu	missense_variant	Exon 3 of 5	3		ENSP00000412005.1
BLVRA	ENST00000453612.1	n.55G>T		non_coding_transcript_exon_variant	Exon 2 of 3	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.39
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.42
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.030	T;T;.
Eigen	Uncertain	0.45
Eigen_PC	Uncertain	0.42
FATHMM_MKL	Uncertain	0.79	D
LIST_S2	Uncertain	0.87	.;D;D
M_CAP	Benign	0.0035	T
MetaRNN	Uncertain	0.44	T;T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	1.8	L;L;.
PrimateAI	Pathogenic	0.83	D
PROVEAN	Benign	-1.4	N;N;N
REVEL	Benign	0.17
Sift	Benign	0.031	D;D;D
Sift4G	Benign	0.19	T;T;T
Polyphen		0.99	D;D;.
Vest4		0.48
MutPred		0.78		Loss of ubiquitination at K8 (P = 0.0613);Loss of ubiquitination at K8 (P = 0.0613);Loss of ubiquitination at K8 (P = 0.0613);
MVP		0.19
MPC		0.77
ClinPred		0.93	D
GERP RS		4.2
Varity_R		0.56
gMVP		0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: rs201359042; hg19: chr7-43827521;