rs162330

Variant names:

• chr2-38092354-C-A
• rs162330
• ENST00000494864.1:c.-71+17315G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-38092354-C-A
• chr2-38092354-C-G
• chr2-38092354-C-T

Variant summary

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

The ENST00000494864.1(CYP1B1):​c.-71+17315G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 152,014 control chromosomes in the GnomAD database, including 20,494 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 0.50 (20494 hom., cov: 32)
• Consequence: CYP1B1 ENST00000494864.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332
• Publications: 11 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 = 0.859 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+17315G>T		intron_variant	Intron 1 of 1	5		ENSP00000479876.1
CYP1B1-AS1	ENST00000589303.6	n.310+15794C>A		intron_variant	Intron 1 of 3	5
CYP1B1-AS1	ENST00000620177.4	n.421+16286C>A		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75798 AN: 151896 Hom.: 20492 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.499 AC: 75825 AN: 152014 Hom.: 20494 Cov.: 32 AF XY: 0.512 AC XY: 38037 AN XY: 74302

African (AFR) AF: 0.310 AC: 12858 AN: 41450

American (AMR) AF: 0.623 AC: 9516 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1565 AN: 3464

East Asian (EAS) AF: 0.880 AC: 4543 AN: 5162

South Asian (SAS) AF: 0.795 AC: 3826 AN: 4810

European-Finnish (FIN) AF: 0.583 AC: 6165 AN: 10582

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.524 AC: 35581 AN: 67954

Other (OTH) AF: 0.536 AC: 1129 AN: 2106

Alfa AF: 0.507 Hom.: 9651

Bravo AF: 0.492

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.3
DANN	Benign	0.83
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs162330; hg19: chr2-38319496;