Variant 2-87719965-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NR_160651.1(ANAPC1P4):n.1013C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000579 in 1,540,796 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0026 ( 9 hom., cov: 22)

Exomes 𝑓: 0.00038 ( 3 hom. )

Consequence

ANAPC1P4
NR_160651.1 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.524

Variant links:

Genes affected

ANAPC1P4 (HGNC:54710): (ANAPC1 pseudogene 4)

ANAPC1P4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 2-87719965-C-T is Benign according to our data. Variant chr2-87719965-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2651106.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 9 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANAPC1P4	NR_160651.1 linkuse as main transcript	n.1013C>T		non_coding_transcript_exon_variant	8/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANAPC1P4	ENST00000427434.2 linkuse as main transcript	n.1078C>T		non_coding_transcript_exon_variant	9/15

Frequencies

GnomAD3 genomes

AF:

0.00259

AC:

367

AN:

141472

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00905

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00138

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00122

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000198

Gnomad OTH

AF:

0.00105

GnomAD3 exomes

AF:

0.000749

AC:

109

AN:

145462

Hom.:

AF XY:

0.000629

AC XY:

AN XY:

77918

show subpopulations

Gnomad AFR exome

AF:

0.00986

Gnomad AMR exome

AF:

0.000434

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000169

Gnomad SAS exome

AF:

0.000335

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000208

Gnomad OTH exome

AF:

0.000712

GnomAD4 exome

AF:

0.000375

AC:

525

AN:

1399214

Hom.:

Cov.:

AF XY:

0.000341

AC XY:

238

AN XY:

696978

show subpopulations

Gnomad4 AFR exome

AF:

0.00743

Gnomad4 AMR exome

AF:

0.000502

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000538

Gnomad4 SAS exome

AF:

0.000230

Gnomad4 FIN exome

AF:

0.0000394

Gnomad4 NFE exome

AF:

0.000175

Gnomad4 OTH exome

AF:

0.000741

GnomAD4 genome

AF:

0.00259

AC:

367

AN:

141582

Hom.:

Cov.:

AF XY:

0.00244

AC XY:

168

AN XY:

68768

show subpopulations

Gnomad4 AFR

AF:

0.00902

Gnomad4 AMR

AF:

0.00138

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00122

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000198

Gnomad4 OTH

AF:

0.00104

Alfa

AF:

0.000129

Hom.:

Bravo

AF:

0.00294

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

ENSG00000284879: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

2.7

DANN

Benign

0.89

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over