rs4670813

Positions:

• chr2-38090568-G-A
• chr2-38090568-G-C

Variant summary

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

The ENST00000629773.2(CYP1B1-AS1):​n.369+14500G>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 0.409 in 152,102 control chromosomes in the GnomAD database, including 15,766 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 0.41 (15766 hom., cov: 33)
• Consequence: CYP1B1-AS1 ENST00000629773.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP1B1-AS1	ENST00000629773.2	n.369+14500G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62240 AN: 151982 Hom.: 15771 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.409 AC: 62237 AN: 152102 Hom.: 15766 Cov.: 33 AF XY: 0.421 AC XY: 31322 AN XY: 74356

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.793

Gnomad4 SAS AF: 0.693

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.448

Alfa AF: 0.335 Hom.: 1711

Bravo AF: 0.397

Asia WGS AF: 0.688 AC: 2390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4670813; hg19: chr2-38317710;