rs1553461069

Variant names:

• chr2-32488593-G-GTCAC
• rs1553461069
• NM_016252.4:c.7976_7979dupCACT

Variant summary

Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1 PM2

The NM_016252.4(BIRC6):​c.7976_7979dupCACT​(p.Leu2661ThrfsTer13) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BIRC6 NM_016252.4 frameshift
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.49
• Publications: 0 publications found

Genes affected

BIRC6 (HGNC:13516): (baculoviral IAP repeat containing 6) This gene encodes a protein with a BIR (baculoviral inhibition of apoptosis protein repeat) domain and a UBCc (ubiquitin-conjugating enzyme E2, catalytic) domain. This protein inhibits apoptosis by facilitating the degradation of apoptotic proteins by ubiquitination. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Pathogenic. The variant received 10 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BIRC6	NM_016252.4	c.7976_7979dupCACT	p.Leu2661ThrfsTer13	frameshift_variant	Exon 42 of 74	ENST00000421745.7	NP_057336.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BIRC6	ENST00000421745.7	c.7976_7979dupCACT	p.Leu2661ThrfsTer13	frameshift_variant	Exon 42 of 74	1	NM_016252.4	ENSP00000393596.2
BIRC6	ENST00000700518.1	c.7925_7928dupCACT	p.Leu2644ThrfsTer13	frameshift_variant	Exon 41 of 73			ENSP00000515025.1
BIRC6	ENST00000700519.1	c.7916_7919dupCACT	p.Leu2641ThrfsTer13	frameshift_variant	Exon 42 of 74			ENSP00000515026.1
BIRC6	ENST00000648282.1	c.7760_7763dupCACT	p.Leu2589fs	frameshift_variant	Exon 41 of 58			ENSP00000498175.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Feb 22, 2017

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1553461069; hg19: chr2-32713660;