rs17022137

Variant names:

• chr2-38152295-T-C
• rs17022137
• ENST00000413828.3:n.214+20681T>C

Variant summary

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

The ENST00000413828.3(CYP1B1-AS1):​n.214+20681T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,090 control chromosomes in the GnomAD database, including 4,590 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 0.24 (4590 hom., cov: 32)
• Consequence: CYP1B1-AS1 ENST00000413828.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP1B1-AS1	NR_027252.1	n.190+20681T>C		intron_variant	Intron 2 of 2
LOC107985871	XR_001739413.2	n.1843-453A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP1B1-AS1	ENST00000413828.3	n.214+20681T>C		intron_variant	Intron 3 of 3	5
ENSG00000227292	ENST00000450854.2	n.1192-30085A>G		intron_variant	Intron 6 of 6	4
CYP1B1-AS1	ENST00000585654.3	n.616+20681T>C		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36517 AN: 151974 Hom.: 4578 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.240 AC: 36563 AN: 152090 Hom.: 4590 Cov.: 32 AF XY: 0.244 AC XY: 18134 AN XY: 74346

African (AFR) AF: 0.291 AC: 12083 AN: 41474

American (AMR) AF: 0.205 AC: 3139 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1041 AN: 3470

East Asian (EAS) AF: 0.110 AC: 572 AN: 5178

South Asian (SAS) AF: 0.287 AC: 1381 AN: 4816

European-Finnish (FIN) AF: 0.247 AC: 2615 AN: 10576

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14798 AN: 67972

Other (OTH) AF: 0.230 AC: 487 AN: 2116

Alfa AF: 0.237 Hom.: 750

Bravo AF: 0.236

Asia WGS AF: 0.226 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.74
DANN	Benign	0.68
PhyloP100		-0.074

Splicing

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

Other links and lift over

dbSNP: rs17022137; hg19: chr2-38379437;