rs10196846

Variant names:

• chr2-38151968-C-A
• rs10196846
• ENST00000413828.3:n.214+20354C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000413828.3(CYP1B1-AS1):​n.214+20354C>A variant causes a intron 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 ENST00000413828.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.609
• Publications: 9 publications found

Genes affected

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

ENSG00000227292 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CYP1B1-AS1	NR_027252.1	n.190+20354C>A		intron_variant	Intron 2 of 2
LOC107985871	XR_001739413.2	n.1843-126G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP1B1-AS1	ENST00000413828.3	n.214+20354C>A		intron_variant	Intron 3 of 3	5
ENSG00000227292	ENST00000450854.2	n.1192-29758G>T		intron_variant	Intron 6 of 6	4
CYP1B1-AS1	ENST00000585654.3	n.616+20354C>A		intron_variant	Intron 3 of 3	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

African (AFR) AF: 0.215 AC: 8902 AN: 41478

American (AMR) AF: 0.166 AC: 2531 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 741 AN: 3472

East Asian (EAS) AF: 0.0599 AC: 310 AN: 5178

South Asian (SAS) AF: 0.227 AC: 1095 AN: 4826

European-Finnish (FIN) AF: 0.195 AC: 2065 AN: 10588

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10562 AN: 67984

Other (OTH) AF: 0.173 AC: 366 AN: 2112

Alfa AF: 0.162 Hom.: 3541

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
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs10196846; hg19: chr2-38379110;