rs9866359

Positions:

• chr3-134479996-T-C
• chr3-134479996-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015391.4(ANAPC13):​c.100-1281A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,258 control chromosomes in the GnomAD database, including 1,797 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 0.15 (1797 hom., cov: 33)
• Consequence: ANAPC13 NM_015391.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619

Genes affected

ANAPC13 (HGNC:24540): (anaphase promoting complex subunit 13) This gene encodes a component of the anaphase promoting complex, a large ubiquitin-protein ligase that controls cell cycle progression by regulating the degradation of cell cycle regulators such as B-type cyclins. The encoded protein is evolutionarily conserved and is required for the integrity and ubiquitin ligase activity of the anaphase promoting complex. Pseudogenes and splice variants have been found for this gene; however, the biological validity of some of the splice variants has not been determined. [provided by RefSeq, Nov 2008]

ANAPC13 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANAPC13	NM_015391.4	c.100-1281A>G		intron_variant		ENST00000354910.10	NP_056206.1
ANAPC13	NM_001242374.1	c.100-1281A>G		intron_variant			NP_001229303.1
ANAPC13	NM_001242375.1	c.100-1281A>G		intron_variant			NP_001229304.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANAPC13	ENST00000354910.10	c.100-1281A>G		intron_variant		1	NM_015391.4	ENSP00000346987.5

Frequencies

GnomAD3 genomes AF: 0.151 AC: 23028 AN: 152140 Hom.: 1794 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.137

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.151 AC: 23035 AN: 152258 Hom.: 1797 Cov.: 33 AF XY: 0.154 AC XY: 11434 AN XY: 74442

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.136

Alfa AF: 0.148 Hom.: 312

Bravo AF: 0.147

Asia WGS AF: 0.211 AC: 736 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.38

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

Other links and lift over

dbSNP: rs9866359; hg19: chr3-134198838;