chr11-102334306-T-C

Variant names:

• chr11-102334306-T-C
• rs7127583
• NM_001165.5:c.1325-1660T>C

Variant summary

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

The NM_001165.5(BIRC3):​c.1325-1660T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,100 control chromosomes in the GnomAD database, including 38,601 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 0.71 (38601 hom., cov: 32)
• Consequence: BIRC3 NM_001165.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479
• Publications: 4 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BIRC3	NM_001165.5	c.1325-1660T>C		intron_variant	Intron 6 of 8	ENST00000263464.9	NP_001156.1
BIRC3	NM_182962.3	c.1325-1660T>C		intron_variant	Intron 7 of 9		NP_892007.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BIRC3	ENST00000263464.9	c.1325-1660T>C		intron_variant	Intron 6 of 8	1	NM_001165.5	ENSP00000263464.4

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107304 AN: 151982 Hom.: 38548 Cov.: 32

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.706 AC: 107419 AN: 152100 Hom.: 38601 Cov.: 32 AF XY: 0.713 AC XY: 53032 AN XY: 74348

African (AFR) AF: 0.821 AC: 34092 AN: 41534

American (AMR) AF: 0.721 AC: 11005 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2328 AN: 3472

East Asian (EAS) AF: 0.759 AC: 3938 AN: 5186

South Asian (SAS) AF: 0.684 AC: 3303 AN: 4826

European-Finnish (FIN) AF: 0.751 AC: 7927 AN: 10558

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42412 AN: 67936

Other (OTH) AF: 0.711 AC: 1504 AN: 2114

Alfa AF: 0.642 Hom.: 37292

Bravo AF: 0.710

Asia WGS AF: 0.755 AC: 2616 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.83
PhyloP100		-0.48
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: rs7127583; hg19: chr11-102205037;