rs3793938

Variant names:

• chr11-72112087-G-A
• rs3793938
• NM_014042.3:c.-96+563C>T

Variant summary

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

The NM_014042.3(ANAPC15):​c.-96+563C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 153,058 control chromosomes in the GnomAD database, including 1,182 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 (1176 hom., cov: 32)
  • Exomes 𝑓: 0.10 (6 hom.)
• Consequence: ANAPC15 NM_014042.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670
• Publications: 3 publications found

Genes affected

ANAPC15 (HGNC:24531): (anaphase promoting complex subunit 15) Involved in regulation of mitotic cell cycle spindle assembly checkpoint. Part of anaphase-promoting complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANAPC15	NM_014042.3	c.-96+563C>T		intron_variant	Intron 1 of 5	ENST00000227618.9	NP_054761.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANAPC15	ENST00000227618.9	c.-96+563C>T		intron_variant	Intron 1 of 5	1	NM_014042.3	ENSP00000227618.4

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16751 AN: 152040 Hom.: 1175 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0900

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0679

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0549

Gnomad OTH AF: 0.0949

GnomAD4 exome AF: 0.102 AC: 92 AN: 900 Hom.: 6 Cov.: 0 AF XY: 0.109 AC XY: 71 AN XY: 654

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.0625 AC: 2 AN: 32

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.134 AC: 71 AN: 530

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0570 AC: 18 AN: 316

Other (OTH) AF: 0.0556 AC: 1 AN: 18

GnomAD4 genome AF: 0.110 AC: 16779 AN: 152158 Hom.: 1176 Cov.: 32 AF XY: 0.115 AC XY: 8558 AN XY: 74374

African (AFR) AF: 0.172 AC: 7127 AN: 41478

American (AMR) AF: 0.172 AC: 2625 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0900 AC: 312 AN: 3468

East Asian (EAS) AF: 0.233 AC: 1203 AN: 5170

South Asian (SAS) AF: 0.162 AC: 780 AN: 4820

European-Finnish (FIN) AF: 0.0679 AC: 720 AN: 10602

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0549 AC: 3734 AN: 68012

Other (OTH) AF: 0.0930 AC: 196 AN: 2108

Alfa AF: 0.0706 Hom.: 854

Bravo AF: 0.118

Asia WGS AF: 0.176 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.1
DANN	Benign	0.66
PhyloP100		0.067
PromoterAI		0.019	Neutral
Mutation Taster		=296/4	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: rs3793938; hg19: chr11-71823133;