rs1324693

Positions:

• chr10-100130860-A-G

Variant summary

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

The ENST00000636357.1(CYP2C23P):​n.321+4491T>C 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 0.274 in 152,154 control chromosomes in the GnomAD database, including 7,062 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 0.27 (7062 hom., cov: 32)
• Consequence: CYP2C23P ENST00000636357.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426

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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 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.321+4491T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41613 AN: 152036 Hom.: 7060 Cov.: 32

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.0661

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.274 AC: 41620 AN: 152154 Hom.: 7062 Cov.: 32 AF XY: 0.268 AC XY: 19934 AN XY: 74382

Gnomad4 AFR AF: 0.0872

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.0657

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.308

Alfa AF: 0.325 Hom.: 1108

Bravo AF: 0.271

Asia WGS AF: 0.115 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.073
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1324693; hg19: chr10-101890617;