2-32532171-G-GTGTGTGTGTGTGTGTGTGTGT

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+621insTGTGTGTGTGTGTGTGTGTGT 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 0.00020 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00014 ( 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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAd4 at 30 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BIRC6NM_016252.4 linkuse as main transcriptc.12291+620_12291+621insTGTGTGTGTGTGTGTGTGTGT intron_variant ENST00000421745.7 NP_057336.3 Q9NR09

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.000201
AC:
30
AN:
149328
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000222
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000133
Gnomad ASJ
AF:
0.000291
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00331
Gnomad NFE
AF:
0.000253
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000141
AC:
53
AN:
376318
Hom.:
0
Cov.:
0
AF XY:
0.000154
AC XY:
33
AN XY:
214488
show subpopulations
Gnomad4 AFR exome
AF:
0.000195
Gnomad4 AMR exome
AF:
0.000168
Gnomad4 ASJ exome
AF:
0.0000864
Gnomad4 EAS exome
AF:
0.000230
Gnomad4 SAS exome
AF:
0.000167
Gnomad4 FIN exome
AF:
0.0000629
Gnomad4 NFE exome
AF:
0.000126
Gnomad4 OTH exome
AF:
0.000244
GnomAD4 genome
AF:
0.000201
AC:
30
AN:
149328
Hom.:
0
Cov.:
0
AF XY:
0.000206
AC XY:
15
AN XY:
72796
show subpopulations
Gnomad4 AFR
AF:
0.000222
Gnomad4 AMR
AF:
0.000133
Gnomad4 ASJ
AF:
0.000291
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000253
Gnomad4 OTH
AF:
0.00

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