Genetic Variant NM_016238.3:c.936-8_936-7dupTT (chr12-110381954-G-GAA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_016238.3(ANAPC7):c.936-8_936-7dupTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00013 ( 0 hom., cov: 0)

Exomes 𝑓: 0.011 ( 6 hom. )

Consequence

ANAPC7
NM_016238.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Variant links:

Genes affected

ANAPC7 (HGNC:17380): (anaphase promoting complex subunit 7) This gene encodes a tetratricopeptide repeat containing component of the anaphase promoting complex/cyclosome (APC/C), a large E3 ubiquitin ligase that controls cell cycle progression by targeting a number of cell cycle regulators such as B-type cyclins for 26S proteasome-mediated degradation through ubiquitination. The encoded protein is required for proper protein ubiquitination function of APC/C and for the interaction of APC/C with certain transcription coactivators. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2008]

ANAPC7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1

Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.011 (9515/865892) while in subpopulation SAS AF= 0.0365 (1673/45832). AF 95% confidence interval is 0.035. There are 6 homozygotes in gnomad4_exome. There are 5089 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Homozygotes in GnomAdExome4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANAPC7	NM_016238.3 link	c.936-8_936-7dupTT		splice_region_variant, intron_variant	Intron 7 of 10	ENST00000455511.9	NP_057322.3	A0A024RBJ3Q4KMX6Q69YV3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANAPC7	ENST00000455511.9 link	c.936-7_936-6insTT		splice_region_variant, intron_variant	Intron 7 of 10	1	NM_016238.3	ENSP00000394394.4		Q9UJX3-1

Frequencies

GnomAD3 genomes

AF:

0.000130

AC:

AN:

107682

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000139

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000190

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0110

AC:

9515

AN:

865892

Hom.:

Cov.:

AF XY:

0.0119

AC XY:

5089

AN XY:

428348

show subpopulations

Gnomad4 AFR exome

AF:

0.00987

Gnomad4 AMR exome

AF:

0.0188

Gnomad4 ASJ exome

AF:

0.0158

Gnomad4 EAS exome

AF:

0.0158

Gnomad4 SAS exome

AF:

0.0365

Gnomad4 FIN exome

AF:

0.0114

Gnomad4 NFE exome

AF:

0.00882

Gnomad4 OTH exome

AF:

0.0117

GnomAD4 genome

AF:

0.000130

AC:

AN:

107658

Hom.:

Cov.:

AF XY:

0.000118

AC XY:

AN XY:

50804

show subpopulations

Gnomad4 AFR

AF:

0.000139

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000190

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over