Variant 6-36330116-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001010903.5(BNIP5):c.575G>A(p.Arg192His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00122 in 1,610,526 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0020 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0011 ( 3 hom. )

Consequence

BNIP5
NM_001010903.5 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.15

Variant links:

Genes affected

BNIP5 (HGNC:33769): (BCL2 interacting protein 5)

BNIP5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004160762).

BP6

Variant 6-36330116-C-T is Benign according to our data. Variant chr6-36330116-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2656514.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BNIP5	NM_001010903.5 linkuse as main transcript	c.575G>A	p.Arg192His	missense_variant	2/12	ENST00000437635.3	NP_001010903.3
BNIP5	XM_011514596.3 linkuse as main transcript	c.575G>A	p.Arg192His	missense_variant	2/12		XP_011512898.1	P0C671
BNIP5	XM_011514597.3 linkuse as main transcript	c.575G>A	p.Arg192His	missense_variant	2/12		XP_011512899.1
BNIP5	XM_011514598.3 linkuse as main transcript	c.-134-1402G>A		intron_variant			XP_011512900.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BNIP5	ENST00000437635.3 linkuse as main transcript	c.575G>A	p.Arg192His	missense_variant	2/12	1	NM_001010903.5	ENSP00000418983.1		P0C671

Frequencies

GnomAD3 genomes

AF:

0.00197

AC:

300

AN:

152148

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00418

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.000654

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.000773

Gnomad SAS

AF:

0.00477

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000867

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00144

AC:

359

AN:

249212

Hom.:

AF XY:

0.00158

AC XY:

213

AN XY:

134900

show subpopulations

Gnomad AFR exome

AF:

0.00394

Gnomad AMR exome

AF:

0.000145

Gnomad ASJ exome

AF:

0.00150

Gnomad EAS exome

AF:

0.000926

Gnomad SAS exome

AF:

0.00501

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000882

Gnomad OTH exome

AF:

0.000819

GnomAD4 exome

AF:

0.00114

AC:

1662

AN:

1458260

Hom.:

Cov.:

AF XY:

0.00128

AC XY:

928

AN XY:

725582

show subpopulations

Gnomad4 AFR exome

AF:

0.00410

Gnomad4 AMR exome

AF:

0.000314

Gnomad4 ASJ exome

AF:

0.00111

Gnomad4 EAS exome

AF:

0.000378

Gnomad4 SAS exome

AF:

0.00537

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000795

Gnomad4 OTH exome

AF:

0.00182

GnomAD4 genome

AF:

0.00197

AC:

300

AN:

152266

Hom.:

Cov.:

AF XY:

0.00201

AC XY:

150

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.00416

Gnomad4 AMR

AF:

0.000653

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.000775

Gnomad4 SAS

AF:

0.00477

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000867

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00117

Hom.:

Bravo

AF:

0.00190

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.000519

AC:

ESP6500AA

AF:

0.00409

AC:

ESP6500EA

AF:

0.000930

AC:

ExAC

AF:

0.00166

AC:

201

Asia WGS

AF:

0.00289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2022

BNIP5: BP4 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.075

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.75

CADD

Benign

0.012

DANN

Benign

0.60

DEOGEN2

Benign

0.010

Eigen

Benign

-1.8

Eigen_PC

Benign

-1.9

FATHMM_MKL

Benign

0.0032

LIST_S2

Benign

0.33

M_CAP

Benign

0.0038

MetaRNN

Benign

0.0042

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.69

PROVEAN

Benign

-0.10

REVEL

Benign

0.0050

Sift

Benign

0.57

Sift4G

Benign

0.55

Polyphen

0.0

Vest4

0.11

MVP

0.014

MPC

0.013

ClinPred

0.00024

GERP RS

-4.9

Varity_R

0.015

gMVP

0.041

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