dbSNP rs1318199: ENSG00000288833:n.449C>G (chr11-102347161-G-C) – 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.449C>G 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 0.0437 in 152,308 control chromosomes in the GnomAD database, including 198 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 0.044 ( 198 hom., cov: 35)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ENSG00000288833
ENST00000687499.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0310

Publications

3 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=-0.72).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0677 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BIRC2	NM_001166.5	MANE Select	c.-1473G>C	upstream_gene	N/A	NP_001157.1	Q13490-1
BIRC2	NM_001256163.1		c.-1942G>C	upstream_gene	N/A	NP_001243092.1	Q13490-1
BIRC2	NM_001256166.2		c.-217G>C	upstream_gene	N/A	NP_001243095.1	Q13490-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ENSG00000288833	ENST00000687499.3		n.449C>G	non_coding_transcript_exon	Exon 1 of 1
ENSG00000288833	ENST00000764978.1		n.39C>G	non_coding_transcript_exon	Exon 1 of 2
BIRC2	ENST00000227758.7	TSL:1 MANE Select	c.-1473G>C	upstream_gene	N/A	ENSP00000227758.2	Q13490-1

Frequencies

GnomAD3 genomes

AF:

0.0438

AC:

6660

AN:

152190

Hom.:

198

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0143

Gnomad AMI

AF:

0.0921

Gnomad AMR

AF:

0.0375

Gnomad ASJ

AF:

0.0689

Gnomad EAS

AF:

0.00540

Gnomad SAS

AF:

0.0174

Gnomad FIN

AF:

0.0231

Gnomad MID

AF:

0.0318

Gnomad NFE

AF:

0.0693

Gnomad OTH

AF:

0.0425

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.0437

AC:

6661

AN:

152308

Hom.:

198

Cov.:

AF XY:

0.0407

AC XY:

3035

AN XY:

74490

show subpopulations

African (AFR)

AF:

0.0143

AC:

594

AN:

41580

American (AMR)

AF:

0.0375

AC:

574

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.0689

AC:

239

AN:

3468

East Asian (EAS)

AF:

0.00560

AC:

AN:

5176

South Asian (SAS)

AF:

0.0174

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.0231

AC:

245

AN:

10620

Middle Eastern (MID)

AF:

0.0308

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0693

AC:

4714

AN:

68004

Other (OTH)

AF:

0.0421

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

337

674

1011

1348

1685

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

228

304

380

<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:

0.0596

Hom.:

Bravo

AF:

0.0429

Asia WGS

AF:

0.0140

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

7.3

(source)

DANN

Benign

0.75

PhyloP100

0.031

PromoterAI

0.14

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

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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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over