Genetic Variant NM_000712.4:c.175T>C (chr7-43791289-T-C) – ACMG Classification: Benign (-15 pts)

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_000712.4(BLVRA):c.175T>C(p.Leu59Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 1,613,934 control chromosomes in the GnomAD database, including 12,140 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 1135 hom., cov: 32)

Exomes 𝑓: 0.12 ( 11005 hom. )

Consequence

BLVRA
NM_000712.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: -0.148

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 -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP6

Variant 7-43791289-T-C is Benign according to our data. Variant chr7-43791289-T-C is described in ClinVar as [Benign]. Clinvar id is 2118007.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.148 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLVRA	NM_000712.4 link	c.175T>C	p.Leu59Leu	synonymous_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.175T>C	p.Leu59Leu	synonymous_variant	Exon 4 of 8	1	NM_000712.4	ENSP00000265523.4	P53004
BLVRA	ENST00000402924.5 link	c.175T>C	p.Leu59Leu	synonymous_variant	Exon 5 of 9	2		ENSP00000385757.1	P53004
BLVRA	ENST00000424330.1 link	c.175T>C	p.Leu59Leu	synonymous_variant	Exon 4 of 5	3		ENSP00000412005.1	C9J1E1
BLVRA	ENST00000453612.1 link	n.199T>C		non_coding_transcript_exon_variant	Exon 3 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.119

AC:

18114

AN:

152022

Hom.:

1130

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.195

Gnomad ASJ

AF:

0.0930

Gnomad EAS

AF:

0.0861

Gnomad SAS

AF:

0.0677

Gnomad FIN

AF:

0.142

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.121

GnomAD3 exomes

AF:

0.127

AC:

31906

AN:

251290

Hom.:

2433

AF XY:

0.120

AC XY:

16245

AN XY:

135794

show subpopulations

Gnomad AFR exome

AF:

0.102

Gnomad AMR exome

AF:

0.255

Gnomad ASJ exome

AF:

0.0864

Gnomad EAS exome

AF:

0.0856

Gnomad SAS exome

AF:

0.0664

Gnomad FIN exome

AF:

0.135

Gnomad NFE exome

AF:

0.117

Gnomad OTH exome

AF:

0.115

GnomAD4 exome

AF:

0.118

AC:

172489

AN:

1461794

Hom.:

11005

Cov.:

AF XY:

0.115

AC XY:

83874

AN XY:

727202

show subpopulations

Gnomad4 AFR exome

AF:

0.0989

Gnomad4 AMR exome

AF:

0.245

Gnomad4 ASJ exome

AF:

0.0888

Gnomad4 EAS exome

AF:

0.0934

Gnomad4 SAS exome

AF:

0.0661

Gnomad4 FIN exome

AF:

0.135

Gnomad4 NFE exome

AF:

0.119

Gnomad4 OTH exome

AF:

0.112

GnomAD4 genome

AF:

0.119

AC:

18153

AN:

152140

Hom.:

1135

Cov.:

AF XY:

0.122

AC XY:

9047

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.102

Gnomad4 AMR

AF:

0.195

Gnomad4 ASJ

AF:

0.0930

Gnomad4 EAS

AF:

0.0861

Gnomad4 SAS

AF:

0.0678

Gnomad4 FIN

AF:

0.142

Gnomad4 NFE

AF:

0.115

Gnomad4 OTH

AF:

0.125

Alfa

AF:

0.115

Hom.:

705

Bravo

AF:

0.126

Asia WGS

AF:

0.113

AC:

393

AN:

3478

EpiCase

AF:

0.109

EpiControl

AF:

0.113

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

BLVRA-related disorder

Benign:1

Oct 22, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not provided

Benign:1

Feb 02, 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

BayesDel_noAF

Benign

-0.58

CADD

Benign

4.4

DANN

Benign

0.71

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