10-100120943-C-T

Position:

• chr10-100120943-C-T

Variant summary

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

The ENST00000636357.1(CYP2C23P):​n.613+5G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 146,876 control chromosomes in the GnomAD database, including 11,311 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 0.39 (11310 hom., cov: 25)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: CYP2C23P ENST00000636357.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20

Genes affected

CYP2C23P (HGNC:):

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 = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP2C23P		n.100120943C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP2C23P	ENST00000636357.1	n.613+5G>A		splice_region_variant, intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.388 AC: 56928 AN: 146790 Hom.: 11298 Cov.: 25

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.448

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.407

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.388 AC: 56987 AN: 146874 Hom.: 11310 Cov.: 25 AF XY: 0.381 AC XY: 27052 AN XY: 71028

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.409

Alfa AF: 0.400 Hom.: 12761

Bravo AF: 0.398

Asia WGS AF: 0.203 AC: 708 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11594333; hg19: chr10-101880700;