chr11-102321236-C-T

Position:

• chr11-102321236-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BIRC3	NM_001165.5	c.-2673-601C>T		intron_variant		ENST00000263464.9	NP_001156.1
BIRC3	NM_182962.3	c.-113-601C>T		intron_variant			NP_892007.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BIRC3	ENST00000263464.9	c.-2673-601C>T		intron_variant		1	NM_001165.5	ENSP00000263464.4

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

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.707

Alfa AF: 0.682 Hom.: 7371

Bravo AF: 0.716

Asia WGS AF: 0.728 AC: 2527 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.34

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

Other links and lift over

dbSNP: rs7928663; hg19: chr11-102191967;