2-32532171-G-GTGTGTGT

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+621insTGTGTGT 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 0.00012 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0024 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

BIRC6
NM_016252.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.931
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAd4 at 18 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BIRC6NM_016252.4 linkc.12291+620_12291+621insTGTGTGT intron_variant ENST00000421745.7 NP_057336.3 Q9NR09

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BIRC6ENST00000421745.7 linkc.12291+620_12291+621insTGTGTGT intron_variant 1 NM_016252.4 ENSP00000393596.2 Q9NR09

Frequencies

GnomAD3 genomes
AF:
0.000121
AC:
18
AN:
149338
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000494
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.000291
Gnomad EAS
AF:
0.000198
Gnomad SAS
AF:
0.000214
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000178
Gnomad OTH
AF:
0.000487
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00237
AC:
893
AN:
376188
Hom.:
0
Cov.:
0
AF XY:
0.00221
AC XY:
473
AN XY:
214434
show subpopulations
Gnomad4 AFR exome
AF:
0.00333
Gnomad4 AMR exome
AF:
0.00599
Gnomad4 ASJ exome
AF:
0.00450
Gnomad4 EAS exome
AF:
0.000614
Gnomad4 SAS exome
AF:
0.00242
Gnomad4 FIN exome
AF:
0.00138
Gnomad4 NFE exome
AF:
0.00178
Gnomad4 OTH exome
AF:
0.00208
GnomAD4 genome
AF:
0.000120
AC:
18
AN:
149456
Hom.:
0
Cov.:
0
AF XY:
0.0000960
AC XY:
7
AN XY:
72926
show subpopulations
Gnomad4 AFR
AF:
0.0000492
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.000291
Gnomad4 EAS
AF:
0.000199
Gnomad4 SAS
AF:
0.000215
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000178
Gnomad4 OTH
AF:
0.000482
Alfa
AF:
0.00476
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs35999329; hg19: chr2-32757238; API