Genetic Variant ENSG00000288833:n.535T>C (chr11-102347075-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000687499.3(ENSG00000288833):n.535T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 24,030 control chromosomes in the GnomAD database, including 655 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 0.51 ( 655 hom., cov: 25)

Exomes 𝑓: 0.083 ( 0 hom. )

Consequence

ENSG00000288833
ENST00000687499.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.941

Publications

2 publications found

Variant links:

Genes affected

ENSG00000288833 (HGNC:):

ENSG00000288833 links:

BIRC2 (HGNC:590): (baculoviral IAP repeat containing 2) The protein encoded by this gene is a member of a family of proteins that inhibits apoptosis by binding to tumor necrosis factor receptor-associated factors TRAF1 and TRAF2, probably by interfering with activation of ICE-like proteases. This encoded protein inhibits apoptosis induced by serum deprivation and menadione, a potent inducer of free radicals. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

BIRC2 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000687499.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687499.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BIRC2	NM_001166.5	MANE Select	c.-1559A>G		upstream_gene	N/A	NP_001157.1	Q13490-1
	BIRC2	NM_001256166.2		c.-303A>G		upstream_gene	N/A	NP_001243095.1	Q13490-2

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
ENSG00000288833	ENST00000687499.3	n.535T>C	non_coding_transcript_exon	Exon 1 of 1
ENSG00000288833	ENST00000764978.1	n.125T>C	non_coding_transcript_exon	Exon 1 of 2
ENSG00000288833	ENST00000764979.1	n.71T>C	non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.508

AC:

12177

AN:

23962

Hom.:

647

Cov.:

show subpopulations

Gnomad AFR

AF:

0.530

Gnomad AMI

AF:

0.519

Gnomad AMR

AF:

0.493

Gnomad ASJ

AF:

0.482

Gnomad EAS

AF:

0.359

Gnomad SAS

AF:

0.413

Gnomad FIN

AF:

0.451

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.493

Gnomad OTH

AF:

0.511

GnomAD4 exome

AF:

0.0833

AC:

AN:

Hom.:

AF XY:

0.0625

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)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0833

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.450

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.509

AC:

12209

AN:

24006

Hom.:

655

Cov.:

AF XY:

0.507

AC XY:

5620

AN XY:

11076

show subpopulations

African (AFR)

AF:

0.531

AC:

5864

AN:

11050

American (AMR)

AF:

0.494

AC:

798

AN:

1616

Ashkenazi Jewish (ASJ)

AF:

0.482

AC:

247

AN:

512

East Asian (EAS)

AF:

0.362

AC:

AN:

South Asian (SAS)

AF:

0.413

AC:

AN:

206

European-Finnish (FIN)

AF:

0.451

AC:

242

AN:

536

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.493

AC:

4712

AN:

9556

Other (OTH)

AF:

0.515

AC:

136

AN:

264

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

565

1130

1696

2261

2826

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

130

260

390

520

650

<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:

0.0369

Hom.:

Bravo

AF:

0.0839

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.7

(source)

DANN

Benign

0.36

PhyloP100

-0.94

PromoterAI

0.073

Neutral

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over