rs232559

Variant names:

• chr2-38169337-T-A
• rs232559
• ENST00000413828.3:n.215-10952T>A

Variant summary

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

The ENST00000450854.2(ENSG00000227292):​n.1191+14993A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,018 control chromosomes in the GnomAD database, including 23,042 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 0.54 (23042 hom., cov: 30)
• Consequence: ENSG00000227292 ENST00000450854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 1 publications found

Genes affected

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

ENSG00000227292 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450854.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP1B1-AS1	NR_027252.1		n.191-10952T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP1B1-AS1	ENST00000413828.3	TSL:5	n.215-10952T>A		intron	N/A
	ENSG00000227292	ENST00000450854.2	TSL:4	n.1191+14993A>T		intron	N/A
	CYP1B1-AS1	ENST00000585654.3	TSL:5	n.617-33171T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82170 AN: 150910 Hom.: 23016 Cov.: 30

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.628

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.545 AC: 82232 AN: 151018 Hom.: 23042 Cov.: 30 AF XY: 0.539 AC XY: 39736 AN XY: 73748

African (AFR) AF: 0.637 AC: 26160 AN: 41072

American (AMR) AF: 0.505 AC: 7665 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2191 AN: 3444

East Asian (EAS) AF: 0.122 AC: 629 AN: 5174

South Asian (SAS) AF: 0.518 AC: 2480 AN: 4788

European-Finnish (FIN) AF: 0.473 AC: 4895 AN: 10348

Middle Eastern (MID) AF: 0.653 AC: 188 AN: 288

European-Non Finnish (NFE) AF: 0.536 AC: 36280 AN: 67720

Other (OTH) AF: 0.558 AC: 1172 AN: 2102

Alfa AF: 0.545 Hom.: 2867

Bravo AF: 0.550

Asia WGS AF: 0.355 AC: 1230 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.44
PhyloP100		0.0090

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs232559;

hg19: chr2-38396479;