rs2567206

Positions:

• chr2-38076389-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000629773.2(CYP1B1-AS1):​n.369+321G>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 0.233 in 164,572 control chromosomes in the GnomAD database, including 5,428 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.23 (4946 hom., cov: 33)
  • Exomes 𝑓: 0.27 (482 hom.)
• Consequence: CYP1B1-AS1 ENST00000629773.2 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.85

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 2-38076389-G-A is Benign according to our data. Variant chr2-38076389-G-A is described in ClinVar as [Benign]. Clinvar id is 1170193.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.355 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+321G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34970 AN: 152044 Hom.: 4947 Cov.: 33

Gnomad AFR AF: 0.0741

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.231

GnomAD4 exome AF: 0.267 AC: 3311 AN: 12414 Hom.: 482 Cov.: 0 AF XY: 0.268 AC XY: 1758 AN XY: 6560

Gnomad4 AFR exome AF: 0.0709

Gnomad4 AMR exome AF: 0.356

Gnomad4 ASJ exome AF: 0.235

Gnomad4 EAS exome AF: 0.107

Gnomad4 SAS exome AF: 0.389

Gnomad4 FIN exome AF: 0.363

Gnomad4 NFE exome AF: 0.277

Gnomad4 OTH exome AF: 0.284

GnomAD4 genome AF: 0.230 AC: 34962 AN: 152158 Hom.: 4946 Cov.: 33 AF XY: 0.238 AC XY: 17666 AN XY: 74380

Gnomad4 AFR AF: 0.0739

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.235

Alfa AF: 0.264 Hom.: 789

Bravo AF: 0.211

Asia WGS AF: 0.268 AC: 932 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Congenital glaucoma Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Oct 13, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.9
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2567206; hg19: chr2-38303531;