ENST00000494864.1:c.-71+17048G>C

Variant names:

• chr2-38092621-C-G
• rs162550
• ENST00000494864.1:c.-71+17048G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000494864.1(CYP1B1):​c.-71+17048G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,046 control chromosomes in the GnomAD database, including 33,271 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 0.63 (33271 hom., cov: 32)
• Consequence: CYP1B1 ENST00000494864.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.596
• Publications: 4 publications found

Genes affected

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]

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP1B1	ENST00000494864.1	c.-71+17048G>C		intron_variant	Intron 1 of 1	5		ENSP00000479876.1
CYP1B1-AS1	ENST00000589303.6	n.310+16061C>G		intron_variant	Intron 1 of 3	5
CYP1B1-AS1	ENST00000620177.4	n.421+16553C>G		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95817 AN: 151928 Hom.: 33268 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.630 AC: 95840 AN: 152046 Hom.: 33271 Cov.: 32 AF XY: 0.639 AC XY: 47519 AN XY: 74322

African (AFR) AF: 0.322 AC: 13348 AN: 41436

American (AMR) AF: 0.775 AC: 11852 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2310 AN: 3470

East Asian (EAS) AF: 0.900 AC: 4665 AN: 5184

South Asian (SAS) AF: 0.890 AC: 4299 AN: 4828

European-Finnish (FIN) AF: 0.713 AC: 7531 AN: 10564

Middle Eastern (MID) AF: 0.747 AC: 218 AN: 292

European-Non Finnish (NFE) AF: 0.729 AC: 49531 AN: 67964

Other (OTH) AF: 0.700 AC: 1477 AN: 2110

Alfa AF: 0.554 Hom.: 1762

Bravo AF: 0.623

Asia WGS AF: 0.853 AC: 2967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.3
DANN	Benign	0.36
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs162550; hg19: chr2-38319763;