3-134481363-C-T

Variant names:

• chr3-134481363-C-T
• rs1863913
• NM_015391.4:c.99+1443G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015391.4(ANAPC13):​c.99+1443G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 152,044 control chromosomes in the GnomAD database, including 31,027 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 0.63 (31027 hom., cov: 32)
• Consequence: ANAPC13 NM_015391.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 21 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANAPC13	NM_015391.4	c.99+1443G>A		intron_variant	Intron 2 of 2	ENST00000354910.10	NP_056206.1
ANAPC13	NM_001242374.1	c.99+1443G>A		intron_variant	Intron 2 of 2		NP_001229303.1
ANAPC13	NM_001242375.1	c.99+1443G>A		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.99+1443G>A		intron_variant	Intron 2 of 2	1	NM_015391.4	ENSP00000346987.5

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95879 AN: 151926 Hom.: 31027 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.631 AC: 95899 AN: 152044 Hom.: 31027 Cov.: 32 AF XY: 0.638 AC XY: 47401 AN XY: 74336

African (AFR) AF: 0.483 AC: 19997 AN: 41414

American (AMR) AF: 0.722 AC: 11042 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2311 AN: 3470

East Asian (EAS) AF: 0.811 AC: 4192 AN: 5170

South Asian (SAS) AF: 0.603 AC: 2907 AN: 4818

European-Finnish (FIN) AF: 0.737 AC: 7796 AN: 10578

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45699 AN: 67984

Other (OTH) AF: 0.633 AC: 1338 AN: 2114

Alfa AF: 0.661 Hom.: 43200

Bravo AF: 0.627

Asia WGS AF: 0.695 AC: 2417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.4
DANN	Benign	0.60
PhyloP100		-0.059
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: rs1863913; hg19: chr3-134200205;