2-32532171-G-GTGTGTGTGTGTGT

Position:

• chr2-32532171-G-GTGTGTGTGTGTGT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_016252.4(BIRC6):​c.12291+620_12291+621insTGTGTGTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00070 (1 hom., cov: 0)
  • Exomes 𝑓: 0.0074 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: BIRC6 NM_016252.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.931

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]

MIR558 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 104 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BIRC6	NM_016252.4	c.12291+620_12291+621insTGTGTGTGTGTGT		intron_variant		ENST00000421745.7	NP_057336.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BIRC6	ENST00000421745.7	c.12291+620_12291+621insTGTGTGTGTGTGT		intron_variant		1	NM_016252.4	ENSP00000393596.2

Frequencies

GnomAD3 genomes AF: 0.000690 AC: 103 AN: 149270 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.000469

Gnomad AMI AF: 0.00111

Gnomad AMR AF: 0.000267

Gnomad ASJ AF: 0.000291

Gnomad EAS AF: 0.000397

Gnomad SAS AF: 0.00107

Gnomad FIN AF: 0.000885

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000893

Gnomad OTH AF: 0.000977

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00742 AC: 2783 AN: 374912 Hom.: 0 Cov.: 0 AF XY: 0.00733 AC XY: 1566 AN XY: 213720

Gnomad4 AFR exome AF: 0.00734

Gnomad4 AMR exome AF: 0.0105

Gnomad4 ASJ exome AF: 0.0134

Gnomad4 EAS exome AF: 0.00292

Gnomad4 SAS exome AF: 0.00761

Gnomad4 FIN exome AF: 0.0157

Gnomad4 NFE exome AF: 0.00550

Gnomad4 OTH exome AF: 0.00582

GnomAD4 genome AF: 0.000696 AC: 104 AN: 149386 Hom.: 1 Cov.: 0 AF XY: 0.000837 AC XY: 61 AN XY: 72890

Gnomad4 AFR AF: 0.000468

Gnomad4 AMR AF: 0.000266

Gnomad4 ASJ AF: 0.000291

Gnomad4 EAS AF: 0.000596

Gnomad4 SAS AF: 0.00107

Gnomad4 FIN AF: 0.000885

Gnomad4 NFE AF: 0.000893

Gnomad4 OTH AF: 0.000966

Alfa AF: 0.0148 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35999329; hg19: chr2-32757238;