dbSNP rs849165: BLVRA:c.13-89G>A (chr7-43787815-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000712.4(BLVRA):c.13-89G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 1,604,566 control chromosomes in the GnomAD database, including 209,324 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 0.55 ( 23233 hom., cov: 31)

Exomes 𝑓: 0.50 ( 186091 hom. )

Consequence

BLVRA
NM_000712.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.853

Publications

17 publications found

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 Gene-Disease associations (from GenCC):

hyperbiliverdinemia
Inheritance: AD, AR, Unknown Classification: MODERATE, SUPPORTIVE, LIMITED Submitted by: Orphanet, ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae)

BLVRA links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000712.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLVRA	NM_000712.4	MANE Select	c.13-89G>A		intron	N/A	NP_000703.2
	BLVRA	NM_001253823.2		c.13-89G>A		intron	N/A	NP_001240752.1	A0A140VJF4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BLVRA	ENST00000265523.9	TSL:1 MANE Select	c.13-89G>A	intron	N/A	ENSP00000265523.4	P53004
BLVRA	ENST00000940902.1		c.13-89G>A	intron	N/A	ENSP00000610961.1
BLVRA	ENST00000854107.1		c.13-89G>A	intron	N/A	ENSP00000524166.1

Frequencies

GnomAD3 genomes

AF:

0.549

AC:

83390

AN:

151762

Hom.:

23201

Cov.:

show subpopulations

Gnomad AFR

AF:

0.641

Gnomad AMI

AF:

0.603

Gnomad AMR

AF:

0.584

Gnomad ASJ

AF:

0.565

Gnomad EAS

AF:

0.494

Gnomad SAS

AF:

0.610

Gnomad FIN

AF:

0.527

Gnomad MID

AF:

0.589

Gnomad NFE

AF:

0.488

Gnomad OTH

AF:

0.545

GnomAD4 exome

AF:

0.503

AC:

731397

AN:

1452686

Hom.:

186091

AF XY:

0.505

AC XY:

365518

AN XY:

723264

show subpopulations

African (AFR)

AF:

0.650

AC:

21632

AN:

33268

American (AMR)

AF:

0.608

AC:

27135

AN:

44614

Ashkenazi Jewish (ASJ)

AF:

0.559

AC:

14561

AN:

26068

East Asian (EAS)

AF:

0.452

AC:

17911

AN:

39616

South Asian (SAS)

AF:

0.599

AC:

51484

AN:

85984

European-Finnish (FIN)

AF:

0.519

AC:

27624

AN:

53214

Middle Eastern (MID)

AF:

0.576

AC:

3312

AN:

5746

European-Non Finnish (NFE)

AF:

0.486

AC:

536288

AN:

1104096

Other (OTH)

AF:

0.523

AC:

31450

AN:

60080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

20409

40817

61226

81634

102043

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15836

31672

47508

63344

79180

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.550

AC:

83479

AN:

151880

Hom.:

23233

Cov.:

AF XY:

0.552

AC XY:

41012

AN XY:

74230

show subpopulations

African (AFR)

AF:

0.641

AC:

26522

AN:

41388

American (AMR)

AF:

0.585

AC:

8922

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.565

AC:

1961

AN:

3470

East Asian (EAS)

AF:

0.495

AC:

2547

AN:

5142

South Asian (SAS)

AF:

0.610

AC:

2938

AN:

4814

European-Finnish (FIN)

AF:

0.527

AC:

5552

AN:

10534

Middle Eastern (MID)

AF:

0.586

AC:

171

AN:

292

European-Non Finnish (NFE)

AF:

0.488

AC:

33163

AN:

67956

Other (OTH)

AF:

0.547

AC:

1153

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1923

3845

5768

7690

9613

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

722

1444

2166

2888

3610

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.509

Hom.:

31797

Bravo

AF:

0.557

Asia WGS

AF:

0.582

AC:

2025

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.10

(source)

DANN

Benign

0.57

PhyloP100

-0.85

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over