rs56058466

chr2-38101728-G-Achr2-38101728-G-Cchr2-38101728-G-T

Variant summary

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

The ENST00000629773.2(CYP1B1-AS1):n.369+25660G>A 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 0.143 in 151,936 control chromosomes in the GnomAD database, including 2,282 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 0.14 (2282 hom., cov: 32)
• Consequence: CYP1B1-AS1 ENST00000629773.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

Genes affected

CYP1B1-AS1 (HGNC:28543): (CYP1B1 antisense RNA 1)

CYP1B1 (HGNC:2597): (cytochrome P450 family 1 subfamily B member 1) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. The enzyme encoded by this gene localizes to the endoplasmic reticulum and metabolizes procarcinogens such as polycyclic aromatic hydrocarbons and 17beta-estradiol. Mutations in this gene have been associated with primary congenital glaucoma; therefore it is thought that the enzyme also metabolizes a signaling molecule involved in eye development, possibly a steroid. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 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
CYP1B1-AS1	ENST00000629773.2	n.369+25660G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21620 AN: 151818 Hom.: 2272 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.0773

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.0724

Gnomad FIN AF: 0.0693

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0868

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.143 AC: 21678 AN: 151936 Hom.: 2282 Cov.: 32 AF XY: 0.138 AC XY: 10274 AN XY: 74256

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.0772

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.0134

Gnomad4 SAS AF: 0.0729

Gnomad4 FIN AF: 0.0693

Gnomad4 NFE AF: 0.0868

Gnomad4 OTH AF: 0.121

Alfa AF: 0.0717 Hom.: 120

Bravo AF: 0.150

Asia WGS AF: 0.0690 AC: 239 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.8
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56058466; hg19: chr2-38328870;