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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450854.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227292	ENST00000450854.2	TSL:4	n.1125+765A>G		intron	N/A
	CYP1B1-AS1	ENST00000585654.3	TSL:5	n.617-16323T>C		intron	N/A
	CYP1B1-AS1	ENST00000589303.6	TSL:5	n.656-16323T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs232593;

hg19: chr2-38413327;