2-32518017-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016252.4(BIRC6):​c.11350-237C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 151,526 control chromosomes in the GnomAD database, including 34,673 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.67 ( 34673 hom., cov: 29)

Consequence

BIRC6
NM_016252.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.238
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 Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BIRC6NM_016252.4 linkc.11350-237C>T intron_variant ENST00000421745.7 NP_057336.3 Q9NR09

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BIRC6ENST00000421745.7 linkc.11350-237C>T intron_variant 1 NM_016252.4 ENSP00000393596.2 Q9NR09

Frequencies

GnomAD3 genomes
AF:
0.668
AC:
101205
AN:
151412
Hom.:
34625
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.786
Gnomad AMI
AF:
0.724
Gnomad AMR
AF:
0.660
Gnomad ASJ
AF:
0.664
Gnomad EAS
AF:
0.311
Gnomad SAS
AF:
0.472
Gnomad FIN
AF:
0.670
Gnomad MID
AF:
0.573
Gnomad NFE
AF:
0.640
Gnomad OTH
AF:
0.658
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.669
AC:
101306
AN:
151526
Hom.:
34673
Cov.:
29
AF XY:
0.665
AC XY:
49252
AN XY:
74028
show subpopulations
Gnomad4 AFR
AF:
0.786
Gnomad4 AMR
AF:
0.660
Gnomad4 ASJ
AF:
0.664
Gnomad4 EAS
AF:
0.310
Gnomad4 SAS
AF:
0.472
Gnomad4 FIN
AF:
0.670
Gnomad4 NFE
AF:
0.640
Gnomad4 OTH
AF:
0.652
Alfa
AF:
0.624
Hom.:
7547
Bravo
AF:
0.676
Asia WGS
AF:
0.414
AC:
1444
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.8
DANN
Benign
0.41

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs2069213; hg19: chr2-32743084; API