ENST00000692445.2:n.286-2027C>T

Variant names:

• chr19-15848390-G-A
• rs2189784
• ENST00000692445.2:n.286-2027C>T

Variant summary

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

The ENST00000692445.2(UCA1-AS1):​n.286-2027C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,852 control chromosomes in the GnomAD database, including 10,438 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 0.36 (10438 hom., cov: 31)
• Consequence: UCA1-AS1 ENST00000692445.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 17 publications found

Genes affected

UCA1-AS1 (HGNC:52553): (UCA1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000692445.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UCA1-AS1	ENST00000692445.2		n.286-2027C>T		intron	N/A
	UCA1-AS1	ENST00000715852.1		n.234+6343C>T		intron	N/A
	UCA1-AS1	ENST00000756861.1		n.213+6343C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55136 AN: 151734 Hom.: 10427 Cov.: 31

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.363 AC: 55186 AN: 151852 Hom.: 10438 Cov.: 31 AF XY: 0.362 AC XY: 26877 AN XY: 74200

African (AFR) AF: 0.272 AC: 11251 AN: 41394

American (AMR) AF: 0.370 AC: 5647 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1528 AN: 3470

East Asian (EAS) AF: 0.305 AC: 1577 AN: 5170

South Asian (SAS) AF: 0.426 AC: 2051 AN: 4810

European-Finnish (FIN) AF: 0.353 AC: 3699 AN: 10488

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28141 AN: 67932

Other (OTH) AF: 0.447 AC: 943 AN: 2110

Alfa AF: 0.400 Hom.: 53058

Bravo AF: 0.358

Asia WGS AF: 0.375 AC: 1305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.29
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs2189784; hg19: chr19-15959200;