Variant rs699512 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_000712.4(BLVRA):c.7G>A(p.Ala3Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 1,612,758 control chromosomes in the GnomAD database, including 495,414 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.83 ( 52420 hom., cov: 32)

Exomes 𝑓: 0.78 ( 442994 hom. )

Consequence

BLVRA
NM_000712.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.538

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=6.306974E-7).

BP6

Variant 7-43771165-G-A is Benign according to our data. Variant chr7-43771165-G-A is described in ClinVar as [Benign]. Clinvar id is 2118005.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-43771165-G-A is described in Lovd as [Benign].

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 linkuse as main transcript	c.7G>A	p.Ala3Thr	missense_variant	2/8	ENST00000265523.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
BLVRA	ENST00000265523.9 linkuse as main transcript	c.7G>A	p.Ala3Thr	missense_variant	2/8	1	NM_000712.4	P1
BLVRA	ENST00000402924.5 linkuse as main transcript	c.7G>A	p.Ala3Thr	missense_variant	3/9	2		P1
BLVRA	ENST00000424330.1 linkuse as main transcript	c.7G>A	p.Ala3Thr	missense_variant	2/5	3
BLVRA	ENST00000453612.1 linkuse as main transcript	n.31G>A		non_coding_transcript_exon_variant	1/3	2

Frequencies

GnomAD3 genomes

AF:

0.826

AC:

125664

AN:

152108

Hom.:

52354

Cov.:

show subpopulations

Gnomad AFR

AF:

0.935

Gnomad AMI

AF:

0.788

Gnomad AMR

AF:

0.857

Gnomad ASJ

AF:

0.792

Gnomad EAS

AF:

0.689

Gnomad SAS

AF:

0.831

Gnomad FIN

AF:

0.803

Gnomad MID

AF:

0.810

Gnomad NFE

AF:

0.769

Gnomad OTH

AF:

0.811

GnomAD3 exomes

AF:

0.801

AC:

201314

AN:

251440

Hom.:

81163

AF XY:

0.799

AC XY:

108533

AN XY:

135888

show subpopulations

Gnomad AFR exome

AF:

0.939

Gnomad AMR exome

AF:

0.877

Gnomad ASJ exome

AF:

0.779

Gnomad EAS exome

AF:

0.694

Gnomad SAS exome

AF:

0.833

Gnomad FIN exome

AF:

0.800

Gnomad NFE exome

AF:

0.768

Gnomad OTH exome

AF:

0.801

GnomAD4 exome

AF:

0.777

AC:

1135417

AN:

1460532

Hom.:

442994

Cov.:

AF XY:

0.778

AC XY:

565512

AN XY:

726668

show subpopulations

Gnomad4 AFR exome

AF:

0.943

Gnomad4 AMR exome

AF:

0.872

Gnomad4 ASJ exome

AF:

0.784

Gnomad4 EAS exome

AF:

0.688

Gnomad4 SAS exome

AF:

0.836

Gnomad4 FIN exome

AF:

0.798

Gnomad4 NFE exome

AF:

0.765

Gnomad4 OTH exome

AF:

0.788

GnomAD4 genome

AF:

0.826

AC:

125796

AN:

152226

Hom.:

52420

Cov.:

AF XY:

0.826

AC XY:

61497

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.935

Gnomad4 AMR

AF:

0.857

Gnomad4 ASJ

AF:

0.792

Gnomad4 EAS

AF:

0.690

Gnomad4 SAS

AF:

0.831

Gnomad4 FIN

AF:

0.803

Gnomad4 NFE

AF:

0.769

Gnomad4 OTH

AF:

0.812

Alfa

AF:

0.781

Hom.:

119889

Bravo

AF:

0.833

TwinsUK

AF:

0.765

AC:

2837

ALSPAC

AF:

0.763

AC:

2941

ESP6500AA

AF:

0.927

AC:

4086

ESP6500EA

AF:

0.765

AC:

6579

ExAC

AF:

0.801

AC:

97244

Asia WGS

AF:

0.775

AC:

2695

AN:

3478

EpiCase

AF:

0.772

EpiControl

AF:

0.772

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.065

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.59

CADD

Benign

6.3

DANN

Benign

0.74

DEOGEN2

Benign

0.015

T;T;.

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.031

LIST_S2

Benign

0.32

.;T;T

MetaRNN

Benign

6.3e-7

T;T;T

MetaSVM

Benign

-0.96

MutationAssessor

Benign

-0.34

N;N;.

MutationTaster

Benign

1.0

P;P

PrimateAI

Uncertain

0.56

PROVEAN

Benign

0.40

N;N;N

REVEL

Benign

0.044

Sift

Benign

0.54

T;T;T

Sift4G

Benign

0.99

T;T;T

Polyphen

0.0

B;B;.

Vest4

0.022

MPC

0.19

ClinPred

0.0036

GERP RS

1.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.024

gMVP

0.51

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