ENST00000457790.1:n.218T>G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.820 AC: 887 AN: 1082

American (AMR) AF: 0.372 AC: 904 AN: 2428

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 275 AN: 388

East Asian (EAS) AF: 0.487 AC: 953 AN: 1958

South Asian (SAS) AF: 0.723 AC: 2356 AN: 3258

European-Finnish (FIN) AF: 0.605 AC: 2444 AN: 4042

Middle Eastern (MID) AF: 0.716 AC: 53 AN: 74

European-Non Finnish (NFE) AF: 0.611 AC: 9564 AN: 15646

Other (OTH) AF: 0.615 AC: 858 AN: 1394

GnomAD4 genome AF: 0.641 AC: 97352 AN: 151964 Hom.: 32118 Cov.: 31 AF XY: 0.638 AC XY: 47347 AN XY: 74248

African (AFR) AF: 0.790 AC: 32792 AN: 41488

American (AMR) AF: 0.522 AC: 7954 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2194 AN: 3468

East Asian (EAS) AF: 0.440 AC: 2270 AN: 5156

South Asian (SAS) AF: 0.668 AC: 3207 AN: 4802

European-Finnish (FIN) AF: 0.576 AC: 6069 AN: 10532

Middle Eastern (MID) AF: 0.771 AC: 225 AN: 292

European-Non Finnish (NFE) AF: 0.598 AC: 40631 AN: 67968

Other (OTH) AF: 0.665 AC: 1400 AN: 2106

Alfa AF: 0.611 Hom.: 122202

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
PhyloP100		-0.20

Splicing

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

Other links and lift over

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