chr11-102328878-ATATT-A

Variant names:

• chr11-102328878-ATATT-A
• NM_001165.5:c.1033-17_1033-14delATTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001165.5(BIRC3):​c.1033-17_1033-14delATTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000268 in 186,656 control chromosomes in the GnomAD database, with no homozygous occurrence. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.000027 (0 hom.)
• Consequence: BIRC3 NM_001165.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

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: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BIRC3	NM_001165.5	c.1033-17_1033-14delATTT		intron_variant	Intron 4 of 8	ENST00000263464.9	NP_001156.1
BIRC3	NM_182962.3	c.1033-17_1033-14delATTT		intron_variant	Intron 5 of 9		NP_892007.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BIRC3	ENST00000263464.9	c.1033-18_1033-15delTATT		intron_variant	Intron 4 of 8	1	NM_001165.5	ENSP00000263464.4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.0000268 AC: 5 AN: 186656 Hom.: 0 AF XY: 0.0000427 AC XY: 4 AN XY: 93694

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 2828

American (AMR) AF: 0.00 AC: 0 AN: 2666

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2418

East Asian (EAS) AF: 0.00 AC: 0 AN: 4160

South Asian (SAS) AF: 0.00 AC: 0 AN: 5798

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3814

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 428

European-Non Finnish (NFE) AF: 0.0000253 AC: 4 AN: 157892

Other (OTH) AF: 0.000150 AC: 1 AN: 6652

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.10

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-102199609;