rs10188379

chr2-38144334-G-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+12720G>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 0.242 in 151,790 control chromosomes in the GnomAD database, including 4,639 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 (4639 hom., cov: 32)
• Consequence: CYP1B1-AS1 NR_027252.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP1B1-AS1	NR_027252.1	n.190+12720G>C		intron_variant, non_coding_transcript_variant
LOC107985871	XR_007086290.1	n.3332+2501C>G		intron_variant, non_coding_transcript_variant
LOC107985871	XR_001739413.2	n.1937-3863C>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+12720G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36734 AN: 151672 Hom.: 4627 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.242 AC: 36782 AN: 151790 Hom.: 4639 Cov.: 32 AF XY: 0.245 AC XY: 18156 AN XY: 74162

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.231

Alfa AF: 0.240 Hom.: 532

Bravo AF: 0.239

Asia WGS AF: 0.234 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.41
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10188379; hg19: chr2-38371476;