rs10196846

chr2-38151968-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.190+20354C>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 0.176 in 152,120 control chromosomes in the GnomAD database, including 2,508 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 0.18 (2508 hom., cov: 32)
• Consequence: CYP1B1-AS1 NR_027252.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.609

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP1B1-AS1	NR_027252.1	n.190+20354C>A		intron_variant, non_coding_transcript_variant
LOC107985871	XR_001739413.2	n.1843-126G>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+20354C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26773 AN: 152002 Hom.: 2498 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0603

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.176 AC: 26803 AN: 152120 Hom.: 2508 Cov.: 32 AF XY: 0.180 AC XY: 13387 AN XY: 74364

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.0599

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.173

Alfa AF: 0.161 Hom.: 2746

Bravo AF: 0.172

Asia WGS AF: 0.156 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.7
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10196846; hg19: chr2-38379110;