rs232559

chr2-38169337-T-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.191-10952T>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 0.545 in 151,018 control chromosomes in the GnomAD database, including 23,042 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 0.54 (23042 hom., cov: 30)
• Consequence: CYP1B1-AS1 NR_027252.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP1B1-AS1	NR_027252.1	n.191-10952T>A		intron_variant, non_coding_transcript_variant
LOC107985871	XR_001739413.2	n.1842+1215A>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+37723T>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82170 AN: 150910 Hom.: 23016 Cov.: 30

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.628

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.545 AC: 82232 AN: 151018 Hom.: 23042 Cov.: 30 AF XY: 0.539 AC XY: 39736 AN XY: 73748

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.558

Alfa AF: 0.545 Hom.: 2867

Bravo AF: 0.550

Asia WGS AF: 0.355 AC: 1230 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.3
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs232559; hg19: chr2-38396479;