dbSNP rs8543: BNIP1:c.*413T>G (chr5-173164334-T-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_001205.3(BNIP1):c.*413T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0896 in 161,344 control chromosomes in the GnomAD database, including 847 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 0.088 ( 774 hom., cov: 32)

Exomes 𝑓: 0.12 ( 73 hom. )

Consequence

BNIP1
NM_001205.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.65

Publications

19 publications found

Variant links:

Genes affected

BNIP1 (HGNC:1082): (BCL2 interacting protein 1) This gene is a member of the BCL2/adenovirus E1B 19 kd-interacting protein (BNIP) family. It interacts with the E1B 19 kDa protein, which protects cells from virally-induced cell death. The encoded protein also interacts with E1B 19 kDa-like sequences of BCL2, another apoptotic protector. In addition, this protein is involved in vesicle transport into the endoplasmic reticulum. Alternative splicing of this gene results in four protein products with identical N- and C-termini. [provided by RefSeq, Mar 2011]

BNIP1 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=-0.52).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BNIP1	NM_001205.3 link	c.*413T>G		3_prime_UTR_variant	Exon 6 of 6	ENST00000351486.10	NP_001196.2	Q12981-4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
BNIP1	ENST00000351486.10 link	c.*413T>G	3_prime_UTR_variant	Exon 6 of 6	1	NM_001205.3	ENSP00000239215.7	Q12981-4
BNIP1	ENST00000231668.13 link	c.*413T>G	3_prime_UTR_variant	Exon 7 of 7	1		ENSP00000231668.9	Q12981-1
BNIP1	ENST00000352523.10 link	c.*413T>G	3_prime_UTR_variant	Exon 6 of 6	1		ENSP00000239214.8	Q12981-3

Frequencies

GnomAD3 genomes

AF:

0.0877

AC:

13352

AN:

152164

Hom.:

775

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0232

Gnomad AMI

AF:

0.0702

Gnomad AMR

AF:

0.0765

Gnomad ASJ

AF:

0.111

Gnomad EAS

AF:

0.0102

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.0898

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.129

Gnomad OTH

AF:

0.104

GnomAD4 exome

AF:

0.121

AC:

1098

AN:

9062

Hom.:

Cov.:

AF XY:

0.122

AC XY:

560

AN XY:

4590

show subpopulations

African (AFR)

AF:

0.0271

AC:

AN:

406

American (AMR)

AF:

0.0551

AC:

AN:

272

Ashkenazi Jewish (ASJ)

AF:

0.124

AC:

AN:

394

East Asian (EAS)

AF:

0.00930

AC:

AN:

430

South Asian (SAS)

AF:

0.128

AC:

AN:

European-Finnish (FIN)

AF:

0.122

AC:

AN:

376

Middle Eastern (MID)

AF:

0.0938

AC:

AN:

European-Non Finnish (NFE)

AF:

0.137

AC:

877

AN:

6412

Other (OTH)

AF:

0.125

AC:

AN:

662

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

146

194

243

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.0877

AC:

13352

AN:

152282

Hom.:

774

Cov.:

AF XY:

0.0867

AC XY:

6457

AN XY:

74454

show subpopulations

African (AFR)

AF:

0.0232

AC:

966

AN:

41574

American (AMR)

AF:

0.0764

AC:

1168

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.111

AC:

386

AN:

3472

East Asian (EAS)

AF:

0.0102

AC:

AN:

5190

South Asian (SAS)

AF:

0.156

AC:

755

AN:

4832

European-Finnish (FIN)

AF:

0.0898

AC:

952

AN:

10602

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.129

AC:

8759

AN:

67998

Other (OTH)

AF:

0.103

AC:

218

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

617

1235

1852

2470

3087

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

166

332

498

664

830

<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:

0.118

Hom.:

1867

Bravo

AF:

0.0811

Asia WGS

AF:

0.0880

AC:

307

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

(source)

DANN

Benign

0.62

PhyloP100

2.7

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