2-32532171-G-GTGTGTGTGTGTGTGTGTGT

Position:

• chr2-32532171-G-GTGTGTGTGTGTGTGTGTGT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_016252.4(BIRC6):​c.12291+620_12291+621insTGTGTGTGTGTGTGTGTGT 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 0.00056 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00049 (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:32814): (microRNA 558) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BIRC6	NM_016252.4	c.12291+620_12291+621insTGTGTGTGTGTGTGTGTGT		intron_variant		ENST00000421745.7	NP_057336.3
MIR558	NR_030285.1	n.19_20insTGTGTGTGTGTGTGTGTGT		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BIRC6	ENST00000421745.7	c.12291+620_12291+621insTGTGTGTGTGTGTGTGTGT		intron_variant		1	NM_016252.4	ENSP00000393596	P2
MIR558	ENST00000384920.1	n.19_20insTGTGTGTGTGTGTGTGTGT		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.000563 AC: 84 AN: 149278 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000518

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000467

Gnomad ASJ AF: 0.00204

Gnomad EAS AF: 0.000594

Gnomad SAS AF: 0.00150

Gnomad FIN AF: 0.000295

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000506

Gnomad OTH AF: 0.000975

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000495 AC: 186 AN: 376108 Hom.: 0 Cov.: 0 AF XY: 0.000438 AC XY: 94 AN XY: 214372

Gnomad4 AFR exome AF: 0.000682

Gnomad4 AMR exome AF: 0.000448

Gnomad4 ASJ exome AF: 0.000520

Gnomad4 EAS exome AF: 0.000690

Gnomad4 SAS exome AF: 0.000576

Gnomad4 FIN exome AF: 0.000409

Gnomad4 NFE exome AF: 0.000452

Gnomad4 OTH exome AF: 0.000611

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000563 AC: 84 AN: 149278 Hom.: 0 Cov.: 0 AF XY: 0.000577 AC XY: 42 AN XY: 72776

Gnomad4 AFR AF: 0.000518

Gnomad4 AMR AF: 0.000467

Gnomad4 ASJ AF: 0.00204

Gnomad4 EAS AF: 0.000594

Gnomad4 SAS AF: 0.00150

Gnomad4 FIN AF: 0.000295

Gnomad4 NFE AF: 0.000506

Gnomad4 OTH AF: 0.000975

Alfa AF: 0.000297 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;