Genetic Variant NM_014042.3:c.-96+563C>T (chr11-72112087-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0670

Publications

3 publications found

Variant links:

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]

ANAPC15 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014042.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ANAPC15	NM_014042.3	MANE Select	c.-96+563C>T	intron	N/A	NP_054761.1
ANAPC15	NM_001393431.1		c.-259C>T	5_prime_UTR	Exon 1 of 6	NP_001380360.1
ANAPC15	NM_001393436.1		c.-259C>T	5_prime_UTR	Exon 1 of 6	NP_001380365.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ANAPC15	ENST00000227618.9	TSL:1 MANE Select	c.-96+563C>T	intron	N/A	ENSP00000227618.4
ANAPC15	ENST00000543587.5	TSL:1	c.-91+563C>T	intron	N/A	ENSP00000439403.1
ANAPC15	ENST00000502597.2	TSL:1	c.-136+563C>T	intron	N/A	ENSP00000441774.1

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16751

AN:

152040

Hom.:

1175

Cov.:

show subpopulations

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:

AN:

900

Hom.:

Cov.:

AF XY:

0.109

AC XY:

AN XY:

654

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.0625

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.134

AC:

AN:

530

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0570

AC:

AN:

316

Other (OTH)

AF:

0.0556

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.110

AC:

16779

AN:

152158

Hom.:

1176

Cov.:

AF XY:

0.115

AC XY:

8558

AN XY:

74374

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.0549

AC:

3734

AN:

68012

Other (OTH)

AF:

0.0930

AC:

196

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

724

1449

2173

2898

3622

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

6.1

(source)

DANN

Benign

0.66

PhyloP100

0.067

PromoterAI

0.019

Neutral

(source)

Mutation Taster

=296/4

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over