4-144850069-G-T

Variant names:

• chr4-144850069-G-T
• rs13102609
• ENST00000649263.1:n.327+214503C>A

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.327+214503C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,046 control chromosomes in the GnomAD database, including 1,494 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 0.11 (1494 hom., cov: 31)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399

Genes affected

ENSG00000285713 (HGNC:):

ANAPC10 (HGNC:24077): (anaphase promoting complex subunit 10) ANAPC10 is a core subunit of the anaphase-promoting complex (APC), or cyclosome, a ubiquitin protein ligase that is essential for progression through the cell cycle. APC initiates sister chromatid separation by ubiquitinating the anaphase inhibitor securin (PTTG1; MIM 604147) and triggers exit from mitosis by ubiquitinating cyclin B (CCNB1; MIM 123836), the activating subunit of cyclin-dependent kinase-1 (CDK1; MIM 116940) (summary by Wendt et al., 2001 [PubMed 11524682]).[supplied by OMIM, Feb 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 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
ENSG00000285713	ENST00000649263.1	n.327+214503C>A		intron_variant	Intron 4 of 8			ENSP00000497507.1
ANAPC10	ENST00000641499.1	n.*55-17151C>A		intron_variant	Intron 5 of 5			ENSP00000493135.1
ENSG00000285783	ENST00000650526.1	n.93+20792C>A		intron_variant	Intron 1 of 14

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16040 AN: 151928 Hom.: 1478 Cov.: 31

Gnomad AFR AF: 0.0390

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.0952

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0845

Gnomad OTH AF: 0.0952

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

GnomAD4 genome AF: 0.106 AC: 16081 AN: 152046 Hom.: 1494 Cov.: 31 AF XY: 0.114 AC XY: 8474 AN XY: 74344

Gnomad4 AFR AF: 0.0391

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.0952

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.0845

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0912 Hom.: 1137

Bravo AF: 0.101

Asia WGS AF: 0.348 AC: 1207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.89
DANN	Benign	0.62

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs13102609; hg19: chr4-145771221;