Genetic Variant BLVRA:p.Gln56Arg (chr7-43791281-A-G) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_000712.4(BLVRA):c.167A>G(p.Gln56Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0105 in 1,614,204 control chromosomes in the GnomAD database, including 121 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.0077 ( 9 hom., cov: 32)

Exomes 𝑓: 0.011 ( 112 hom. )

Consequence

BLVRA
NM_000712.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 4.68

Variant links:

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]

BLVRA links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.007294029).

BP6

Variant 7-43791281-A-G is Benign according to our data. Variant chr7-43791281-A-G is described in ClinVar as [Benign]. Clinvar id is 775081.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 9 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLVRA	NM_000712.4 link	c.167A>G	p.Gln56Arg	missense_variant	Exon 4 of 8	ENST00000265523.9	NP_000703.2	P53004A0A140VJF4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
BLVRA	ENST00000265523.9 link	c.167A>G	p.Gln56Arg	missense_variant	Exon 4 of 8	1	NM_000712.4	ENSP00000265523.4	P53004
BLVRA	ENST00000402924.5 link	c.167A>G	p.Gln56Arg	missense_variant	Exon 5 of 9	2		ENSP00000385757.1	P53004
BLVRA	ENST00000424330.1 link	c.167A>G	p.Gln56Arg	missense_variant	Exon 4 of 5	3		ENSP00000412005.1	C9J1E1
BLVRA	ENST00000453612.1 link	n.191A>G		non_coding_transcript_exon_variant	Exon 3 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.00769

AC:

1170

AN:

152212

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00162

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.00249

Gnomad ASJ

AF:

0.00288

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00331

Gnomad FIN

AF:

0.0219

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0115

Gnomad OTH

AF:

0.00575

GnomAD3 exomes

AF:

0.00801

AC:

2012

AN:

251312

Hom.:

AF XY:

0.00811

AC XY:

1102

AN XY:

135808

show subpopulations

Gnomad AFR exome

AF:

0.00154

Gnomad AMR exome

AF:

0.00289

Gnomad ASJ exome

AF:

0.00298

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00519

Gnomad FIN exome

AF:

0.0258

Gnomad NFE exome

AF:

0.00967

Gnomad OTH exome

AF:

0.00669

GnomAD4 exome

AF:

0.0108

AC:

15757

AN:

1461874

Hom.:

112

Cov.:

AF XY:

0.0106

AC XY:

7673

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.00102

Gnomad4 AMR exome

AF:

0.00264

Gnomad4 ASJ exome

AF:

0.00310

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00590

Gnomad4 FIN exome

AF:

0.0269

Gnomad4 NFE exome

AF:

0.0117

Gnomad4 OTH exome

AF:

0.00944

GnomAD4 genome

AF:

0.00768

AC:

1170

AN:

152330

Hom.:

Cov.:

AF XY:

0.00810

AC XY:

603

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.00161

Gnomad4 AMR

AF:

0.00248

Gnomad4 ASJ

AF:

0.00288

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00332

Gnomad4 FIN

AF:

0.0219

Gnomad4 NFE

AF:

0.0115

Gnomad4 OTH

AF:

0.00569

Alfa

AF:

0.00946

Hom.:

Bravo

AF:

0.00584

TwinsUK

AF:

0.0127

AC:

ALSPAC

AF:

0.0112

AC:

ESP6500AA

AF:

0.00227

AC:

ESP6500EA

AF:

0.0108

AC:

ExAC

AF:

0.00766

AC:

930

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.00878

EpiControl

AF:

0.00990

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Sep 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

BLVRA: BS1, BS2 -

Jan 13, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Benign

-0.43

BayesDel_noAF

Benign

-0.38

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.033

T;T;.

Eigen

Uncertain

0.47

Eigen_PC

Uncertain

0.47

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.81

.;T;T

MetaRNN

Benign

0.0073

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.7

L;L;.

PrimateAI

Uncertain

0.55

PROVEAN

Benign

-2.2

N;N;N

REVEL

Benign

0.14

Sift

Uncertain

0.010

D;D;T

Sift4G

Pathogenic

0.0

D;D;D

Polyphen

1.0

D;D;.

Vest4

0.61

MVP

0.22

MPC

0.81

ClinPred

0.012

GERP RS

4.8

Varity_R

0.67

gMVP

0.76

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over