rs232593

Variant names:

• chr2-38186185-T-C
• rs232593
• ENST00000450854.2:n.1125+765A>G

Variant summary

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

The ENST00000450854.2(ENSG00000227292):​n.1125+765A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,168 control chromosomes in the GnomAD database, including 7,532 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 0.31 (7532 hom., cov: 33)
• Consequence: ENSG00000227292 ENST00000450854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.719
• Publications: 1 publications found

Genes affected

ENSG00000227292 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723739	XR_007086289.1	n.13856+765A>G		intron_variant	Intron 3 of 3
LOC102723739	XR_427020.4	n.302+765A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227292	ENST00000450854.2	n.1125+765A>G		intron_variant	Intron 5 of 6	4
CYP1B1-AS1	ENST00000585654.3	n.617-16323T>C		intron_variant	Intron 3 of 3	5
CYP1B1-AS1	ENST00000589303.6	n.656-16323T>C		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47389 AN: 152050 Hom.: 7521 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.312 AC: 47429 AN: 152168 Hom.: 7532 Cov.: 33 AF XY: 0.307 AC XY: 22824 AN XY: 74398

African (AFR) AF: 0.298 AC: 12365 AN: 41512

American (AMR) AF: 0.287 AC: 4379 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1371 AN: 3468

East Asian (EAS) AF: 0.109 AC: 565 AN: 5184

South Asian (SAS) AF: 0.300 AC: 1446 AN: 4822

European-Finnish (FIN) AF: 0.255 AC: 2698 AN: 10600

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23400 AN: 67982

Other (OTH) AF: 0.329 AC: 695 AN: 2110

Alfa AF: 0.334 Hom.: 1777

Bravo AF: 0.313

Asia WGS AF: 0.237 AC: 823 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.69
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs232593; hg19: chr2-38413327;