NM_015391.4:c.100-1281A>G

Variant names:

• chr3-134479996-T-C
• rs9866359
• NM_015391.4:c.100-1281A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ANAPC13	NM_015391.4	c.100-1281A>G		intron_variant	Intron 2 of 2	ENST00000354910.10	NP_056206.1
ANAPC13	NM_001242374.1	c.100-1281A>G		intron_variant	Intron 2 of 2		NP_001229303.1
ANAPC13	NM_001242375.1	c.100-1281A>G		intron_variant	Intron 2 of 2		NP_001229304.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANAPC13	ENST00000354910.10	c.100-1281A>G		intron_variant	Intron 2 of 2	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

African (AFR) AF: 0.126 AC: 5230 AN: 41566

American (AMR) AF: 0.148 AC: 2257 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 359 AN: 3472

East Asian (EAS) AF: 0.202 AC: 1046 AN: 5182

South Asian (SAS) AF: 0.184 AC: 887 AN: 4828

European-Finnish (FIN) AF: 0.217 AC: 2295 AN: 10580

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10553 AN: 68016

Other (OTH) AF: 0.136 AC: 287 AN: 2114

Alfa AF: 0.147 Hom.: 320

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
PhyloP100		-0.62
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9866359; hg19: chr3-134198838;