rs17022137

chr2-38152295-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_027252.1(CYP1B1-AS1):n.190+20681T>C variant causes a intron, non coding transcript 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 NR_027252.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740

Genes affected

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

LOC107985871 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CYP1B1-AS1	NR_027252.1	n.190+20681T>C		intron_variant, non_coding_transcript_variant
LOC107985871	XR_001739413.2	n.1843-453A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP1B1-AS1	ENST00000629773.2	n.473+20681T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.230

Alfa AF: 0.235 Hom.: 718

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17022137; hg19: chr2-38379437;