rs2862990

Positions:

• chr10-100116607-C-T

Variant summary

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

The ENST00000636357.1(CYP2C23P):​n.787+663G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 152,036 control chromosomes in the GnomAD database, including 11,288 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 0.38 (11288 hom., cov: 32)
• Consequence: CYP2C23P ENST00000636357.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

CYP2C23P (HGNC:39970): (cytochrome P450 family 2 subfamily C member 23, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP2C23P	ENST00000636357.1	n.787+663G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57947 AN: 151918 Hom.: 11277 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.397

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.382 AC: 58005 AN: 152036 Hom.: 11288 Cov.: 32 AF XY: 0.376 AC XY: 27908 AN XY: 74298

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.325

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.398

Alfa AF: 0.390 Hom.: 2199

Bravo AF: 0.390

Asia WGS AF: 0.204 AC: 711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.24
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2862990; hg19: chr10-101876364; COSMIC: COSV71418945;