rs10188379

Variant names:

• chr2-38144334-G-C
• rs10188379
• ENST00000413828.3:n.214+12720G>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+12720G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 151,790 control chromosomes in the GnomAD database, including 4,639 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 (4639 hom., cov: 32)
• Consequence: CYP1B1-AS1 ENST00000413828.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672
• Publications: 7 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413828.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP1B1-AS1	NR_027252.1		n.190+12720G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP1B1-AS1	ENST00000413828.3	TSL:5	n.214+12720G>C		intron	N/A
	ENSG00000227292	ENST00000450854.2	TSL:4	n.1192-22124C>G		intron	N/A
	CYP1B1-AS1	ENST00000585654.3	TSL:5	n.616+12720G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36734 AN: 151672 Hom.: 4627 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.242 AC: 36782 AN: 151790 Hom.: 4639 Cov.: 32 AF XY: 0.245 AC XY: 18156 AN XY: 74162

African (AFR) AF: 0.299 AC: 12382 AN: 41356

American (AMR) AF: 0.206 AC: 3150 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1006 AN: 3464

East Asian (EAS) AF: 0.140 AC: 722 AN: 5158

South Asian (SAS) AF: 0.288 AC: 1385 AN: 4816

European-Finnish (FIN) AF: 0.248 AC: 2606 AN: 10500

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14580 AN: 67906

Other (OTH) AF: 0.231 AC: 487 AN: 2112

Alfa AF: 0.240 Hom.: 532

Bravo AF: 0.239

Asia WGS AF: 0.234 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.56
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs10188379; hg19: chr2-38371476;