Variant rs2239680 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001168.3(BIRC5):c.*148T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 1,447,208 control chromosomes in the GnomAD database, including 53,845 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 0.24 ( 4545 hom., cov: 33)

Exomes 𝑓: 0.27 ( 49300 hom. )

Consequence

BIRC5
NM_001168.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.747

Variant links:

Genes affected

BIRC5 (HGNC:593): (baculoviral IAP repeat containing 5) This gene is a member of the inhibitor of apoptosis (IAP) gene family, which encode negative regulatory proteins that prevent apoptotic cell death. IAP family members usually contain multiple baculovirus IAP repeat (BIR) domains, but this gene encodes proteins with only a single BIR domain. The encoded proteins also lack a C-terminus RING finger domain. Gene expression is high during fetal development and in most tumors, yet low in adult tissues. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jun 2011]

BIRC5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
BIRC5	NM_001168.3 linkuse as main transcript	c.*148T>C	3_prime_UTR_variant	4/4	ENST00000350051.8	NP_001159.2
BIRC5	NM_001012270.2 linkuse as main transcript	c.*45T>C	3_prime_UTR_variant	3/3		NP_001012270.1
BIRC5	NM_001012271.2 linkuse as main transcript	c.*148T>C	3_prime_UTR_variant	5/5		NP_001012271.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BIRC5	ENST00000350051.8 linkuse as main transcript	c.*148T>C	3_prime_UTR_variant	4/4	1	NM_001168.3	ENSP00000324180	P1
BIRC5	ENST00000301633.8 linkuse as main transcript	c.*148T>C	3_prime_UTR_variant	5/5	1		ENSP00000301633
BIRC5	ENST00000374948.6 linkuse as main transcript	c.*45T>C	3_prime_UTR_variant	3/3	1		ENSP00000364086		O15392-3
BIRC5	ENST00000589892.1 linkuse as main transcript	n.593T>C	non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.238

AC:

36177

AN:

151860

Hom.:

4541

Cov.:

show subpopulations

Gnomad AFR

AF:

0.168

Gnomad AMI

AF:

0.480

Gnomad AMR

AF:

0.190

Gnomad ASJ

AF:

0.228

Gnomad EAS

AF:

0.256

Gnomad SAS

AF:

0.225

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.229

GnomAD3 exomes

AF:

0.270

AC:

26095

AN:

96698

Hom.:

3387

AF XY:

0.274

AC XY:

13890

AN XY:

50748

show subpopulations

Gnomad AFR exome

AF:

0.166

Gnomad AMR exome

AF:

0.174

Gnomad ASJ exome

AF:

0.249

Gnomad EAS exome

AF:

0.264

Gnomad SAS exome

AF:

0.251

Gnomad FIN exome

AF:

0.298

Gnomad NFE exome

AF:

0.307

Gnomad OTH exome

AF:

0.281

GnomAD4 exome

AF:

0.273

AC:

354009

AN:

1295230

Hom.:

49300

Cov.:

AF XY:

0.272

AC XY:

171331

AN XY:

629766

show subpopulations

Gnomad4 AFR exome

AF:

0.166

Gnomad4 AMR exome

AF:

0.163

Gnomad4 ASJ exome

AF:

0.225

Gnomad4 EAS exome

AF:

0.255

Gnomad4 SAS exome

AF:

0.228

Gnomad4 FIN exome

AF:

0.281

Gnomad4 NFE exome

AF:

0.283

Gnomad4 OTH exome

AF:

0.259

GnomAD4 genome

AF:

0.238

AC:

36203

AN:

151978

Hom.:

4545

Cov.:

AF XY:

0.240

AC XY:

17827

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.168

Gnomad4 AMR

AF:

0.189

Gnomad4 ASJ

AF:

0.228

Gnomad4 EAS

AF:

0.257

Gnomad4 SAS

AF:

0.228

Gnomad4 FIN

AF:

0.292

Gnomad4 NFE

AF:

0.280

Gnomad4 OTH

AF:

0.231

Alfa

AF:

0.258

Hom.:

3750

Bravo

AF:

0.224

Asia WGS

AF:

0.244

AC:

851

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.2

DANN

Benign

0.64

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over