Variant 2-111769289-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_022662.4(ANAPC1):c.*2C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 1,603,028 control chromosomes in the GnomAD database, including 38,764 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2650 hom., cov: 27)

Exomes 𝑓: 0.22 ( 36114 hom. )

Consequence

ANAPC1
NM_022662.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.240

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]

ANAPC1 links:

ANAPC1 (HGNC:):

ANAPC1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 2-111769289-G-A is Benign according to our data. Variant chr2-111769289-G-A is described in ClinVar as [Benign]. Clinvar id is 1188976.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANAPC1	NM_022662.4 linkuse as main transcript	c.*2C>T		3_prime_UTR_variant	48/48	ENST00000341068.8	NP_073153.1	Q9H1A4

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ANAPC1	ENST00000341068 linkuse as main transcript	c.*2C>T	3_prime_UTR_variant	48/48	1	NM_022662.4	ENSP00000339109.3	Q9H1A4
ANAPC1	ENST00000427997.5 linkuse as main transcript	c.4322-2294C>T	intron_variant		1		ENSP00000396695.1	H0Y564
ANAPC1	ENST00000462785.1 linkuse as main transcript	n.2531C>T	non_coding_transcript_exon_variant	4/4	2
ANAPC1	ENST00000643447.1 linkuse as main transcript	n.746-2294C>T	intron_variant				ENSP00000494863.1	A0A2R8YF63

Frequencies

GnomAD3 genomes

AF:

0.178

AC:

26923

AN:

151246

Hom.:

2648

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0896

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.179

Gnomad ASJ

AF:

0.231

Gnomad EAS

AF:

0.158

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.160

Gnomad MID

AF:

0.287

Gnomad NFE

AF:

0.230

Gnomad OTH

AF:

0.200

GnomAD3 exomes

AF:

0.204

AC:

49851

AN:

244616

Hom.:

5421

AF XY:

0.212

AC XY:

27979

AN XY:

132278

show subpopulations

Gnomad AFR exome

AF:

0.0871

Gnomad AMR exome

AF:

0.169

Gnomad ASJ exome

AF:

0.234

Gnomad EAS exome

AF:

0.175

Gnomad SAS exome

AF:

0.227

Gnomad FIN exome

AF:

0.162

Gnomad NFE exome

AF:

0.233

Gnomad OTH exome

AF:

0.230

GnomAD4 exome

AF:

0.221

AC:

320388

AN:

1451662

Hom.:

36114

Cov.:

AF XY:

0.221

AC XY:

159817

AN XY:

721538

show subpopulations

Gnomad4 AFR exome

AF:

0.0828

Gnomad4 AMR exome

AF:

0.167

Gnomad4 ASJ exome

AF:

0.226

Gnomad4 EAS exome

AF:

0.155

Gnomad4 SAS exome

AF:

0.225

Gnomad4 FIN exome

AF:

0.163

Gnomad4 NFE exome

AF:

0.231

Gnomad4 OTH exome

AF:

0.218

GnomAD4 genome

AF:

0.178

AC:

26935

AN:

151366

Hom.:

2650

Cov.:

AF XY:

0.175

AC XY:

12932

AN XY:

73902

show subpopulations

Gnomad4 AFR

AF:

0.0895

Gnomad4 AMR

AF:

0.179

Gnomad4 ASJ

AF:

0.231

Gnomad4 EAS

AF:

0.158

Gnomad4 SAS

AF:

0.196

Gnomad4 FIN

AF:

0.160

Gnomad4 NFE

AF:

0.230

Gnomad4 OTH

AF:

0.201

Alfa

AF:

0.203

Hom.:

729

Bravo

AF:

0.178

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Rothmund-Thomson syndrome type 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.8

DANN

Benign

0.89

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over