chr2-38170300-C-A

Variant names:

• chr2-38170300-C-A
• rs2447741
• ENST00000413828.3:n.215-9989C>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.215-9989C>A variant causes a intron 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 ENST00000413828.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378
• Publications: 6 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=-0.8).
• 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 rank	MANE	Protein	UniProt
CYP1B1-AS1	NR_027252.1	n.191-9989C>A		intron_variant	Intron 2 of 2
LOC107985871	XR_001739413.2	n.1842+252G>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.215-9989C>A		intron_variant	Intron 3 of 3	5
ENSG00000227292	ENST00000450854.2	n.1191+14030G>T		intron_variant	Intron 6 of 6	4
CYP1B1-AS1	ENST00000585654.3	n.617-32208C>A		intron_variant	Intron 3 of 3	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

African (AFR) AF: 0.653 AC: 27097 AN: 41482

American (AMR) AF: 0.480 AC: 7341 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1998 AN: 3466

East Asian (EAS) AF: 0.143 AC: 741 AN: 5164

South Asian (SAS) AF: 0.470 AC: 2264 AN: 4814

European-Finnish (FIN) AF: 0.442 AC: 4648 AN: 10518

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32942 AN: 67946

Other (OTH) AF: 0.541 AC: 1142 AN: 2110

Alfa AF: 0.500 Hom.: 14781

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
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs2447741; hg19: chr2-38397442;