ENST00000457790.1:n.218T>G

Variant names:

• chr10-95007177-A-C
• rs2860975
• ENST00000457790.1:n.218T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200

Genes affected

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

ACMG classification

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2C59P	ENST00000457790.1	n.218T>G		non_coding_transcript_exon_variant	Exon 2 of 2	6

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97253 AN: 151846 Hom.: 32073 Cov.: 31

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.: 0 AF XY: 0.617 AC XY: 11043 AN XY: 17892

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.: 31 AF XY: 0.638 AC XY: 47347 AN XY: 74248

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

Other links and lift over

dbSNP: rs2860975; hg19: chr10-96766934; COSMIC: COSV71960215;