2-111712578-C-T

Variant summary

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

The ENST00000643447.1(ANAPC1):​n.*139+17701G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,192 control chromosomes in the GnomAD database, including 8,240 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 0.31 ( 8240 hom., cov: 33)

Consequence

ANAPC1
ENST00000643447.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0400
Variant links:
Genes affected
ANAPC1 (HGNC:19988): (anaphase promoting complex subunit 1) This gene encodes a subunit of the anaphase-promoting complex. This complex is an E3 ubiquitin ligase that regulates progression through the metaphase to anaphase portion of the cell cycle by ubiquitinating proteins which targets them for degradation. [provided by RefSeq, Dec 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ANAPC1ENST00000643447.1 linkn.*139+17701G>A intron_variant Intron 9 of 11 ENSP00000494863.1 A0A2R8YF63

Frequencies

GnomAD3 genomes
AF:
0.309
AC:
47045
AN:
152074
Hom.:
8242
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.164
Gnomad AMI
AF:
0.461
Gnomad AMR
AF:
0.287
Gnomad ASJ
AF:
0.387
Gnomad EAS
AF:
0.150
Gnomad SAS
AF:
0.311
Gnomad FIN
AF:
0.340
Gnomad MID
AF:
0.418
Gnomad NFE
AF:
0.403
Gnomad OTH
AF:
0.331
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.309
AC:
47054
AN:
152192
Hom.:
8240
Cov.:
33
AF XY:
0.306
AC XY:
22792
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.164
Gnomad4 AMR
AF:
0.287
Gnomad4 ASJ
AF:
0.387
Gnomad4 EAS
AF:
0.150
Gnomad4 SAS
AF:
0.311
Gnomad4 FIN
AF:
0.340
Gnomad4 NFE
AF:
0.403
Gnomad4 OTH
AF:
0.330
Alfa
AF:
0.301
Hom.:
1423
Bravo
AF:
0.298
Asia WGS
AF:
0.219
AC:
767
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
4.0
DANN
Benign
0.77

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: rs11122895; hg19: chr2-112470155; API