chr2-38078309-A-G

Position:

• chr2-38078309-A-G

Variant summary

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

The ENST00000629773.2(CYP1B1-AS1):​n.369+2241A>G 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 0.781 in 152,030 control chromosomes in the GnomAD database, including 46,562 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 0.78 (46562 hom., cov: 31)
• Consequence: CYP1B1-AS1 ENST00000629773.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615

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=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.892 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+2241A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118611 AN: 151912 Hom.: 46535 Cov.: 31

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.781 AC: 118697 AN: 152030 Hom.: 46562 Cov.: 31 AF XY: 0.785 AC XY: 58351 AN XY: 74302

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.758

Gnomad4 OTH AF: 0.810

Alfa AF: 0.767 Hom.: 11978

Bravo AF: 0.789

Asia WGS AF: 0.900 AC: 3131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	10
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs162557; hg19: chr2-38305451;