rs183487

Variant names:

• chr2-38187399-T-C
• rs183487
• XR_007086289.1:n.13407A>G

Variant summary

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

The XR_007086289.1(LOC102723739):​n.13407A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,644 control chromosomes in the GnomAD database, including 4,372 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 0.23 (4372 hom., cov: 30)
• Consequence: LOC102723739 XR_007086289.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 2 publications found

Genes affected

LOC102723739 (HGNC:):

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227292	ENST00000450854.2	TSL:4	n.997-321A>G		intron	N/A
	CYP1B1-AS1	ENST00000585654.3	TSL:5	n.617-15109T>C		intron	N/A
	CYP1B1-AS1	ENST00000589303.6	TSL:5	n.656-15109T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35578 AN: 151526 Hom.: 4368 Cov.: 30

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.0551

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.235 AC: 35603 AN: 151644 Hom.: 4372 Cov.: 30 AF XY: 0.233 AC XY: 17244 AN XY: 74096

African (AFR) AF: 0.183 AC: 7561 AN: 41318

American (AMR) AF: 0.239 AC: 3645 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1079 AN: 3460

East Asian (EAS) AF: 0.0548 AC: 284 AN: 5180

South Asian (SAS) AF: 0.249 AC: 1189 AN: 4784

European-Finnish (FIN) AF: 0.210 AC: 2199 AN: 10484

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18775 AN: 67876

Other (OTH) AF: 0.251 AC: 527 AN: 2096

Alfa AF: 0.267 Hom.: 4493

Bravo AF: 0.233

Asia WGS AF: 0.178 AC: 618 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.5
DANN	Benign	0.74
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs183487; hg19: chr2-38414541;