rs162556

Positions:

• chr2-38079312-G-A

Variant summary

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

The ENST00000629773.2(CYP1B1-AS1):​n.369+3244G>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 0.616 in 152,198 control chromosomes in the GnomAD database, including 31,452 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 0.62 (31452 hom., cov: 33)
• Consequence: CYP1B1-AS1 ENST00000629773.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 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+3244G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93627 AN: 152080 Hom.: 31395 Cov.: 33

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.616 AC: 93743 AN: 152198 Hom.: 31452 Cov.: 33 AF XY: 0.610 AC XY: 45427 AN XY: 74414

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.586

Alfa AF: 0.547 Hom.: 31553

Bravo AF: 0.627

Asia WGS AF: 0.408 AC: 1423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.80
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs162556; hg19: chr2-38306454;