rs2447741

Positions:

• chr2-38170300-C-A

Variant summary

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

The NR_027252.1(CYP1B1-AS1):​n.191-9989C>A 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 0.518 in 151,992 control chromosomes in the GnomAD database, including 21,341 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 0.52 (21341 hom., cov: 32)
• Consequence: CYP1B1-AS1 NR_027252.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP1B1-AS1	NR_027252.1	n.191-9989C>A		intron_variant, non_coding_transcript_variant
LOC107985871	XR_001739413.2	n.1842+252G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP1B1-AS1	ENST00000629773.2	n.473+38686C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78721 AN: 151874 Hom.: 21312 Cov.: 32

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.518 AC: 78791 AN: 151992 Hom.: 21341 Cov.: 32 AF XY: 0.514 AC XY: 38138 AN XY: 74270

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.541

Alfa AF: 0.497 Hom.: 11012

Bravo AF: 0.526

Asia WGS AF: 0.347 AC: 1202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.9
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2447741; hg19: chr2-38397442;