2-203300448-T-C

Variant names:

• chr2-203300448-T-C
• rs11888559
• NM_177538.3:c.*3540T>C

Variant summary

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

The NM_177538.3(CYP20A1):​c.*3540T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.819 in 152,142 control chromosomes in the GnomAD database, including 53,647 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 0.82 (53647 hom., cov: 33)
• Consequence: CYP20A1 NM_177538.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

Genes affected

CYP20A1 (HGNC:20576): (cytochrome P450 family 20 subfamily A member 1) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases that catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein lacks one amino acid of the conserved heme binding site. It also lacks the conserved I-helix motif AGX(D,E)T, suggesting that its substrate may carry its own oxygen. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP20A1	NM_177538.3	c.*3540T>C		3_prime_UTR_variant	Exon 13 of 13	ENST00000356079.9	NP_803882.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP20A1	ENST00000356079.9	c.*3540T>C		3_prime_UTR_variant	Exon 13 of 13	1	NM_177538.3	ENSP00000348380.4

Frequencies

GnomAD3 genomes AF: 0.819 AC: 124492 AN: 152024 Hom.: 53639 Cov.: 33

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.979

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.956

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.950

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.819 AC: 124544 AN: 152142 Hom.: 53647 Cov.: 33 AF XY: 0.821 AC XY: 61018 AN XY: 74366

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.874

Gnomad4 ASJ AF: 0.963

Gnomad4 EAS AF: 0.834

Gnomad4 SAS AF: 0.867

Gnomad4 FIN AF: 0.956

Gnomad4 NFE AF: 0.950

Gnomad4 OTH AF: 0.851

Alfa AF: 0.929 Hom.: 137175

Bravo AF: 0.798

Asia WGS AF: 0.813 AC: 2829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11888559; hg19: chr2-204165171;