dbSNP rs1042542: BIRC5:c.*1793T>C (chr17-78225347-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001012271.2(BIRC5):c.*1793T>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 0.638 in 152,118 control chromosomes in the GnomAD database, including 30,987 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 0.64 ( 30986 hom., cov: 33)

Exomes 𝑓: 0.63 ( 1 hom. )

Consequence

BIRC5
NM_001012271.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.499

Publications

14 publications found

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:

ENSG00000308650 (HGNC:):

ENSG00000308650 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001012271.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BIRC5	NM_001168.3	MANE Select	c.*1793T>C	3_prime_UTR	Exon 4 of 4	NP_001159.2
BIRC5	NM_001012271.2		c.*1793T>C	3_prime_UTR	Exon 5 of 5	NP_001012271.1
BIRC5	NM_001012270.2		c.*1690T>C	3_prime_UTR	Exon 3 of 3	NP_001012270.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BIRC5	ENST00000350051.8	TSL:1 MANE Select	c.*1793T>C	3_prime_UTR	Exon 4 of 4	ENSP00000324180.4
BIRC5	ENST00000301633.8	TSL:1	c.*1793T>C	3_prime_UTR	Exon 5 of 5	ENSP00000301633.3
BIRC5	ENST00000374948.6	TSL:1	c.*1690T>C	3_prime_UTR	Exon 3 of 3	ENSP00000364086.1

Frequencies

GnomAD3 genomes

AF:

0.638

AC:

96905

AN:

151992

Hom.:

30961

Cov.:

show subpopulations

Gnomad AFR

AF:

0.619

Gnomad AMI

AF:

0.691

Gnomad AMR

AF:

0.604

Gnomad ASJ

AF:

0.644

Gnomad EAS

AF:

0.641

Gnomad SAS

AF:

0.665

Gnomad FIN

AF:

0.640

Gnomad MID

AF:

0.766

Gnomad NFE

AF:

0.652

Gnomad OTH

AF:

0.628

GnomAD4 exome

AF:

0.625

AC:

AN:

Hom.:

Cov.:

AF XY:

0.625

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.667

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.642

Heterozygous variant carriers

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:

0.638

AC:

96983

AN:

152110

Hom.:

30986

Cov.:

AF XY:

0.639

AC XY:

47491

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.619

AC:

25687

AN:

41484

American (AMR)

AF:

0.605

AC:

9240

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.644

AC:

2235

AN:

3472

East Asian (EAS)

AF:

0.641

AC:

3314

AN:

5174

South Asian (SAS)

AF:

0.666

AC:

3209

AN:

4820

European-Finnish (FIN)

AF:

0.640

AC:

6769

AN:

10570

Middle Eastern (MID)

AF:

0.762

AC:

224

AN:

294

European-Non Finnish (NFE)

AF:

0.652

AC:

44352

AN:

67996

Other (OTH)

AF:

0.628

AC:

1324

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1881

3762

5642

7523

9404

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

800

1600

2400

3200

4000

<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:

0.641

Hom.:

84161

Bravo

AF:

0.629

Asia WGS

AF:

0.639

AC:

2225

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.1

(source)

DANN

Benign

0.20

PhyloP100

-0.50

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over