2-111712578-C-T

Variant names:

• chr2-111712578-C-T
• rs11122895
• ENST00000643447.1:n.*139+17701G>A

Variant summary

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

The ENST00000643447.1(ANAPC1):​n.*139+17701G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,192 control chromosomes in the GnomAD database, including 8,240 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 0.31 (8240 hom., cov: 33)
• Consequence: ANAPC1 ENST00000643447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

Genes affected

ANAPC1 (HGNC:19988): (anaphase promoting complex subunit 1) This gene encodes a subunit of the anaphase-promoting complex. This complex is an E3 ubiquitin ligase that regulates progression through the metaphase to anaphase portion of the cell cycle by ubiquitinating proteins which targets them for degradation. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.399 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
ANAPC1	ENST00000643447.1	n.*139+17701G>A		intron_variant	Intron 9 of 11			ENSP00000494863.1

Frequencies

GnomAD3 genomes AF: 0.309 AC: 47045 AN: 152074 Hom.: 8242 Cov.: 33

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.309 AC: 47054 AN: 152192 Hom.: 8240 Cov.: 33 AF XY: 0.306 AC XY: 22792 AN XY: 74388

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.330

Alfa AF: 0.301 Hom.: 1423

Bravo AF: 0.298

Asia WGS AF: 0.219 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11122895; hg19: chr2-112470155;