10-100120943-C-T

Variant names:

• chr10-100120943-C-T
• rs11594333

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000636357.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP2C23P	ENST00000636357.1	TSL:6	n.613+5G>A		splice_region intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.416 AC: 16544 AN: 39814

American (AMR) AF: 0.386 AC: 5571 AN: 14434

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1197 AN: 3456

East Asian (EAS) AF: 0.138 AC: 696 AN: 5060

South Asian (SAS) AF: 0.231 AC: 1081 AN: 4670

European-Finnish (FIN) AF: 0.311 AC: 2789 AN: 8974

Middle Eastern (MID) AF: 0.444 AC: 127 AN: 286

European-Non Finnish (NFE) AF: 0.411 AC: 27657 AN: 67254

Other (OTH) AF: 0.409 AC: 829 AN: 2028

Alfa AF: 0.398 Hom.: 34616

Bravo AF: 0.398

Asia WGS AF: 0.203 AC: 708 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.21
PhyloP100		-2.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11594333;

hg19: chr10-101880700;