chr10-95007177-A-C

Position:

• chr10-95007177-A-C

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/exons	MANE	Protein	UniProt

Ensembl

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

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;