4-144850069-G-T

Variant names:

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

Variant summary

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

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649263.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285713	ENST00000649263.1		n.327+214503C>A		intron	N/A	ENSP00000497507.1
	ANAPC10	ENST00000641499.1		n.*55-17151C>A		intron	N/A	ENSP00000493135.1
	ENSG00000285783	ENST00000650526.1		n.93+20792C>A		intron	N/A

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

African (AFR) AF: 0.0391 AC: 1624 AN: 41520

American (AMR) AF: 0.181 AC: 2765 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0952 AC: 330 AN: 3468

East Asian (EAS) AF: 0.435 AC: 2230 AN: 5132

South Asian (SAS) AF: 0.243 AC: 1172 AN: 4816

European-Finnish (FIN) AF: 0.177 AC: 1870 AN: 10576

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0845 AC: 5745 AN: 67956

Other (OTH) AF: 0.103 AC: 217 AN: 2112

Alfa AF: 0.0895 Hom.: 1699

Bravo AF: 0.101

Asia WGS AF: 0.348 AC: 1207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.89
DANN	Benign	0.62
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs13102609; hg19: chr4-145771221;