Variant rs2860975 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000457790.1(CYP2C59P):n.218T>G 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 0.635 in 182,234 control chromosomes in the GnomAD database, including 37,733 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 0.64 ( 32118 hom., cov: 31)

Exomes 𝑓: 0.60 ( 5615 hom. )

Consequence

CYP2C59P
ENST00000457790.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.200

Variant links:

Genes affected

CYP2C59P (HGNC:42406): (cytochrome P450 family 2 subfamily C member 59, pseudogene)

CYP2C59P links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP2C59P	ENST00000457790.1 linkuse as main transcript	n.218T>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes

AF:

0.640

AC:

97253

AN:

151846

Hom.:

32073

Cov.:

show subpopulations

Gnomad AFR

AF:

0.790

Gnomad AMI

AF:

0.672

Gnomad AMR

AF:

0.523

Gnomad ASJ

AF:

0.633

Gnomad EAS

AF:

0.440

Gnomad SAS

AF:

0.667

Gnomad FIN

AF:

0.576

Gnomad MID

AF:

0.774

Gnomad NFE

AF:

0.598

Gnomad OTH

AF:

0.662

GnomAD4 exome

AF:

0.604

AC:

18294

AN:

30270

Hom.:

5615

Cov.:

AF XY:

0.617

AC XY:

11043

AN XY:

17892

show subpopulations

Gnomad4 AFR exome

AF:

0.820

Gnomad4 AMR exome

AF:

0.372

Gnomad4 ASJ exome

AF:

0.709

Gnomad4 EAS exome

AF:

0.487

Gnomad4 SAS exome

AF:

0.723

Gnomad4 FIN exome

AF:

0.605

Gnomad4 NFE exome

AF:

0.611

Gnomad4 OTH exome

AF:

0.615

GnomAD4 genome

AF:

0.641

AC:

97352

AN:

151964

Hom.:

32118

Cov.:

AF XY:

0.638

AC XY:

47347

AN XY:

74248

show subpopulations

Gnomad4 AFR

AF:

0.790

Gnomad4 AMR

AF:

0.522

Gnomad4 ASJ

AF:

0.633

Gnomad4 EAS

AF:

0.440

Gnomad4 SAS

AF:

0.668

Gnomad4 FIN

AF:

0.576

Gnomad4 NFE

AF:

0.598

Gnomad4 OTH

AF:

0.665

Alfa

AF:

0.609

Hom.:

57833

Bravo

AF:

0.638

Asia WGS

AF:

0.590

AC:

2052

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

1.7

DANN

Benign

0.62

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