chr11-72112087-G-A

Variant summary

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

The ENST00000227618.9(ANAPC15):​c.-96+563C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 153,058 control chromosomes in the GnomAD database, including 1,182 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 0.11 ( 1176 hom., cov: 32)
Exomes 𝑓: 0.10 ( 6 hom. )

Consequence

ANAPC15
ENST00000227618.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0670
Variant links:
Genes affected
ANAPC15 (HGNC:24531): (anaphase promoting complex subunit 15) Involved in regulation of mitotic cell cycle spindle assembly checkpoint. Part of anaphase-promoting complex. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ANAPC15NM_014042.3 linkuse as main transcriptc.-96+563C>T intron_variant ENST00000227618.9 NP_054761.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ANAPC15ENST00000227618.9 linkuse as main transcriptc.-96+563C>T intron_variant 1 NM_014042.3 ENSP00000227618 P1P60006-1

Frequencies

GnomAD3 genomes
AF:
0.110
AC:
16751
AN:
152040
Hom.:
1175
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.172
Gnomad AMI
AF:
0.0570
Gnomad AMR
AF:
0.171
Gnomad ASJ
AF:
0.0900
Gnomad EAS
AF:
0.233
Gnomad SAS
AF:
0.161
Gnomad FIN
AF:
0.0679
Gnomad MID
AF:
0.0949
Gnomad NFE
AF:
0.0549
Gnomad OTH
AF:
0.0949
GnomAD4 exome
AF:
0.102
AC:
92
AN:
900
Hom.:
6
Cov.:
0
AF XY:
0.109
AC XY:
71
AN XY:
654
show subpopulations
Gnomad4 AMR exome
AF:
0.0625
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.134
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0570
Gnomad4 OTH exome
AF:
0.0556
GnomAD4 genome
AF:
0.110
AC:
16779
AN:
152158
Hom.:
1176
Cov.:
32
AF XY:
0.115
AC XY:
8558
AN XY:
74374
show subpopulations
Gnomad4 AFR
AF:
0.172
Gnomad4 AMR
AF:
0.172
Gnomad4 ASJ
AF:
0.0900
Gnomad4 EAS
AF:
0.233
Gnomad4 SAS
AF:
0.162
Gnomad4 FIN
AF:
0.0679
Gnomad4 NFE
AF:
0.0549
Gnomad4 OTH
AF:
0.0930
Alfa
AF:
0.0661
Hom.:
605
Bravo
AF:
0.118
Asia WGS
AF:
0.176
AC:
613
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
6.1
DANN
Benign
0.66

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: rs3793938; hg19: chr11-71823133; API