2-32532171-G-GTGTGTGTGTGTGTGT

Position:

• chr2-32532171-G-GTGTGTGTGTGTGTGT

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+621insTGTGTGTGTGTGTGT 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 0.0011 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0039 (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 163 AD gene.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.00109 AC: 163 AN: 149240 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000592

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00133

Gnomad ASJ AF: 0.00116

Gnomad EAS AF: 0.000992

Gnomad SAS AF: 0.000858

Gnomad FIN AF: 0.000787

Gnomad MID AF: 0.00331

Gnomad NFE AF: 0.00141

Gnomad OTH AF: 0.000976

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00394 AC: 1479 AN: 375282 Hom.: 0 Cov.: 0 AF XY: 0.00387 AC XY: 827 AN XY: 213936

Gnomad4 AFR exome AF: 0.00390

Gnomad4 AMR exome AF: 0.00407

Gnomad4 ASJ exome AF: 0.00634

Gnomad4 EAS exome AF: 0.00192

Gnomad4 SAS exome AF: 0.00389

Gnomad4 FIN exome AF: 0.00851

Gnomad4 NFE exome AF: 0.00323

Gnomad4 OTH exome AF: 0.00300

GnomAD4 genome AF: 0.00109 AC: 163 AN: 149356 Hom.: 0 Cov.: 0 AF XY: 0.00110 AC XY: 80 AN XY: 72878

Gnomad4 AFR AF: 0.000591

Gnomad4 AMR AF: 0.00133

Gnomad4 ASJ AF: 0.00116

Gnomad4 EAS AF: 0.000995

Gnomad4 SAS AF: 0.000859

Gnomad4 FIN AF: 0.000787

Gnomad4 NFE AF: 0.00141

Gnomad4 OTH AF: 0.000965

Alfa AF: 0.0126 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;