dbSNP rs10233867: BLVRA:c.-21-3468A>G (chr7-43767670-A-G) – 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.-21-3468A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 609,330 control chromosomes in the GnomAD database, including 10,114 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 0.14 ( 2157 hom., cov: 32)

Exomes 𝑓: 0.18 ( 7957 hom. )

Consequence

BLVRA
NM_000712.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.193

Publications

7 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, Unknown Classification: SUPPORTIVE, LIMITED Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics

BLVRA links:

LOC107986727 (HGNC:):

LOC107986727 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=-0.73).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLVRA	NM_000712.4 link	c.-21-3468A>G		intron_variant	Intron 1 of 7	ENST00000265523.9	NP_000703.2	P53004A0A140VJF4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
BLVRA	ENST00000265523.9 link	c.-21-3468A>G	intron_variant	Intron 1 of 7	1	NM_000712.4	ENSP00000265523.4	P53004
BLVRA	ENST00000402924.5 link	c.-21-3468A>G	intron_variant	Intron 2 of 8	2		ENSP00000385757.1	P53004
BLVRA	ENST00000424330.1 link	c.-22+3365A>G	intron_variant	Intron 1 of 4	3		ENSP00000412005.1	C9J1E1
ENSG00000229497	ENST00000431286.1 link	n.*71A>G	downstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

22052

AN:

152056

Hom.:

2157

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0377

Gnomad AMI

AF:

0.0614

Gnomad AMR

AF:

0.128

Gnomad ASJ

AF:

0.181

Gnomad EAS

AF:

0.00788

Gnomad SAS

AF:

0.116

Gnomad FIN

AF:

0.227

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.213

Gnomad OTH

AF:

0.147

GnomAD4 exome

AF:

0.178

AC:

81336

AN:

457156

Hom.:

7957

AF XY:

0.178

AC XY:

44935

AN XY:

252672

show subpopulations

African (AFR)

AF:

0.0346

AC:

430

AN:

12434

American (AMR)

AF:

0.0998

AC:

3085

AN:

30912

Ashkenazi Jewish (ASJ)

AF:

0.188

AC:

2501

AN:

13288

East Asian (EAS)

AF:

0.00572

AC:

104

AN:

18192

South Asian (SAS)

AF:

0.127

AC:

7901

AN:

62284

European-Finnish (FIN)

AF:

0.220

AC:

4921

AN:

22324

Middle Eastern (MID)

AF:

0.171

AC:

274

AN:

1598

European-Non Finnish (NFE)

AF:

0.213

AC:

58336

AN:

274402

Other (OTH)

AF:

0.174

AC:

3784

AN:

21722

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

3301

6602

9904

13205

16506

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

742

1484

2226

2968

3710

<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:

0.145

AC:

22043

AN:

152174

Hom.:

2157

Cov.:

AF XY:

0.142

AC XY:

10535

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.0376

AC:

1561

AN:

41550

American (AMR)

AF:

0.127

AC:

1945

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.181

AC:

629

AN:

3468

East Asian (EAS)

AF:

0.00790

AC:

AN:

5192

South Asian (SAS)

AF:

0.115

AC:

553

AN:

4818

European-Finnish (FIN)

AF:

0.227

AC:

2401

AN:

10572

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.213

AC:

14510

AN:

67970

Other (OTH)

AF:

0.145

AC:

306

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

916

1831

2747

3662

4578

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

250

500

750

1000

1250

<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:

0.176

Hom.:

404

Bravo

AF:

0.132

Asia WGS

AF:

0.0620

AC:

218

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

(source)

DANN

Benign

0.96

PhyloP100

-0.19

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over