Variant chr2-32357173-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_016252.4(BIRC6):c.12T>C(p.Gly4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 1,525,628 control chromosomes in the GnomAD database, including 399 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.032 ( 164 hom., cov: 32)

Exomes 𝑓: 0.013 ( 235 hom. )

Consequence

BIRC6
NM_016252.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.0640

Variant links:

Genes affected

BIRC6 (HGNC:13516): (baculoviral IAP repeat containing 6) This gene encodes a protein with a BIR (baculoviral inhibition of apoptosis protein repeat) domain and a UBCc (ubiquitin-conjugating enzyme E2, catalytic) domain. This protein inhibits apoptosis by facilitating the degradation of apoptotic proteins by ubiquitination. [provided by RefSeq, Jul 2008]

BIRC6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP6

Variant 2-32357173-T-C is Benign according to our data. Variant chr2-32357173-T-C is described in ClinVar as [Benign]. Clinvar id is 3037379.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.064 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BIRC6	NM_016252.4 linkuse as main transcript	c.12T>C	p.Gly4=	synonymous_variant	1/74	ENST00000421745.7	NP_057336.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
BIRC6	ENST00000421745.7 linkuse as main transcript	c.12T>C	p.Gly4=	synonymous_variant	1/74	1	NM_016252.4	ENSP00000393596	P2
BIRC6	ENST00000700518.1 linkuse as main transcript	c.12T>C	p.Gly4=	synonymous_variant	1/73			ENSP00000515025	A2
BIRC6	ENST00000700519.1 linkuse as main transcript	c.12T>C	p.Gly4=	synonymous_variant	1/74			ENSP00000515026

Frequencies

GnomAD3 genomes

AF:

0.0316

AC:

4814

AN:

152126

Hom.:

163

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0868

Gnomad AMI

AF:

0.0252

Gnomad AMR

AF:

0.0155

Gnomad ASJ

AF:

0.00692

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.00331

Gnomad FIN

AF:

0.00236

Gnomad MID

AF:

0.0223

Gnomad NFE

AF:

0.0124

Gnomad OTH

AF:

0.0201

GnomAD3 exomes

AF:

0.00950

AC:

1318

AN:

138700

Hom.:

AF XY:

0.00917

AC XY:

716

AN XY:

78114

show subpopulations

Gnomad AFR exome

AF:

0.0757

Gnomad AMR exome

AF:

0.00680

Gnomad ASJ exome

AF:

0.00649

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00443

Gnomad FIN exome

AF:

0.00291

Gnomad NFE exome

AF:

0.0105

Gnomad OTH exome

AF:

0.00594

GnomAD4 exome

AF:

0.0130

AC:

17902

AN:

1373394

Hom.:

235

Cov.:

AF XY:

0.0127

AC XY:

8629

AN XY:

680438

show subpopulations

Gnomad4 AFR exome

AF:

0.0896

Gnomad4 AMR exome

AF:

0.00848

Gnomad4 ASJ exome

AF:

0.00707

Gnomad4 EAS exome

AF:

0.0000311

Gnomad4 SAS exome

AF:

0.00443

Gnomad4 FIN exome

AF:

0.00292

Gnomad4 NFE exome

AF:

0.0126

Gnomad4 OTH exome

AF:

0.0148

GnomAD4 genome

AF:

0.0317

AC:

4828

AN:

152234

Hom.:

164

Cov.:

AF XY:

0.0312

AC XY:

2322

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.0869

Gnomad4 AMR

AF:

0.0155

Gnomad4 ASJ

AF:

0.00692

Gnomad4 EAS

AF:

0.000387

Gnomad4 SAS

AF:

0.00352

Gnomad4 FIN

AF:

0.00236

Gnomad4 NFE

AF:

0.0124

Gnomad4 OTH

AF:

0.0198

Alfa

AF:

0.0168

Hom.:

Bravo

AF:

0.0353

Asia WGS

AF:

0.00694

AC:

AN:

3472

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

BIRC6-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 19, 2019

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). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

DANN

Benign

0.79

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

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