dbSNP rs2189784: UCA1-AS1:n.286-2027C>T (chr19-15848390-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.18

Publications

17 publications found

Variant links:

Genes affected

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

UCA1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
UCA1-AS1	ENST00000692445.2 link	n.286-2027C>T	intron_variant	Intron 2 of 2
UCA1-AS1	ENST00000715852.1 link	n.234+6343C>T	intron_variant	Intron 2 of 2
UCA1-AS1	ENST00000756861.1 link	n.213+6343C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.363

AC:

55136

AN:

151734

Hom.:

10427

Cov.:

show subpopulations

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.:

AF XY:

0.362

AC XY:

26877

AN XY:

74200

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1766

3532

5297

7063

8829

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

552

1104

1656

2208

2760

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.56

(source)

DANN

Benign

0.29

PhyloP100

-2.2

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over