chr10-94872496-T-C

Position:

• chr10-94872496-T-C

Variant summary

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

The variant allele was found at a frequency of 0.58 in 152,080 control chromosomes in the GnomAD database, including 26,291 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 0.58 (26291 hom., cov: 33)
• Consequence: CYP2C58P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

CYP2C58P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP2C58P		n.94872496T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP2C58P	ENST00000436281.1	n.172+462A>G		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88205 AN: 151962 Hom.: 26276 Cov.: 33

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.580 AC: 88260 AN: 152080 Hom.: 26291 Cov.: 33 AF XY: 0.579 AC XY: 43053 AN XY: 74340

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.572

Alfa AF: 0.564 Hom.: 24531

Bravo AF: 0.572

Asia WGS AF: 0.544 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.83
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4466755; hg19: chr10-96632253;