11-102321236-C-T

Variant names:

• chr11-102321236-C-T
• rs7928663
• NM_001165.5:c.-2673-601C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001165.5(BIRC3):​c.-2673-601C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 152,150 control chromosomes in the GnomAD database, including 39,938 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 0.72 (39938 hom., cov: 33)
• Consequence: BIRC3 NM_001165.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540
• Publications: 3 publications found

Genes affected

BIRC3 (HGNC:591): (baculoviral IAP repeat containing 3) This gene encodes a member of the IAP family of proteins that inhibit apoptosis by binding to tumor necrosis factor receptor-associated factors TRAF1 and TRAF2, probably by interfering with activation of ICE-like proteases. The encoded protein inhibits apoptosis induced by serum deprivation but does not affect apoptosis resulting from exposure to menadione, a potent inducer of free radicals. It contains 3 baculovirus IAP repeats and a ring finger domain. Transcript variants encoding the same isoform have been identified. [provided by RefSeq, Aug 2011]

ENSG00000288528 (HGNC:):

ACMG classification

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 = 0.834 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001165.5. 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
	BIRC3	NM_001165.5	MANE Select	c.-2673-601C>T		intron	N/A	NP_001156.1	Q13489
	BIRC3	NM_182962.3		c.-113-601C>T		intron	N/A	NP_892007.1	Q13489

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BIRC3	ENST00000263464.9	TSL:1 MANE Select	c.-2673-601C>T		intron	N/A	ENSP00000263464.4	Q13489
	BIRC3	ENST00000673846.1		c.-2673-601C>T		intron	N/A	ENSP00000501181.1	A0A669KBC7
	BIRC3	ENST00000526421.6	TSL:2	c.-2673-601C>T		intron	N/A	ENSP00000501119.1	Q13489

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109393 AN: 152032 Hom.: 39881 Cov.: 33

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.704

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.720 AC: 109511 AN: 152150 Hom.: 39938 Cov.: 33 AF XY: 0.723 AC XY: 53745 AN XY: 74378

African (AFR) AF: 0.841 AC: 34943 AN: 41538

American (AMR) AF: 0.643 AC: 9818 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2408 AN: 3466

East Asian (EAS) AF: 0.722 AC: 3736 AN: 5174

South Asian (SAS) AF: 0.685 AC: 3301 AN: 4820

European-Finnish (FIN) AF: 0.778 AC: 8221 AN: 10570

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44674 AN: 67986

Other (OTH) AF: 0.707 AC: 1495 AN: 2114

Alfa AF: 0.680 Hom.: 12251

Bravo AF: 0.716

Asia WGS AF: 0.728 AC: 2527 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.34
PhyloP100		0.054
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7928663; hg19: chr11-102191967;