Genetic Variant ADAMTS19-AS1:n.1031+3356G>A (chr5-129443666-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000661962.1(ADAMTS19-AS1):n.1031+3356G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,082 control chromosomes in the GnomAD database, including 1,740 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 0.14 ( 1740 hom., cov: 32)

Consequence

ADAMTS19-AS1
ENST00000661962.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.01

Publications

5 publications found

Variant links:

Genes affected

ADAMTS19-AS1 (HGNC:40797): (ADAMTS19 antisense RNA 1)

ADAMTS19-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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ADAMTS19-AS1	ENST00000661962.1 link	n.1031+3356G>A	intron_variant	Intron 3 of 3
ADAMTS19-AS1	ENST00000723046.1 link	n.136+3356G>A	intron_variant	Intron 2 of 2
ADAMTS19-AS1	ENST00000723047.1 link	n.1061+3356G>A	intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes

AF:

0.139

AC:

21085

AN:

151964

Hom.:

1740

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.0647

Gnomad AMR

AF:

0.118

Gnomad ASJ

AF:

0.106

Gnomad EAS

AF:

0.362

Gnomad SAS

AF:

0.150

Gnomad FIN

AF:

0.0866

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.134

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

GnomAD4 genome

AF:

0.139

AC:

21092

AN:

152082

Hom.:

1740

Cov.:

AF XY:

0.139

AC XY:

10345

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.186

AC:

7717

AN:

41476

American (AMR)

AF:

0.118

AC:

1794

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.106

AC:

369

AN:

3470

East Asian (EAS)

AF:

0.362

AC:

1871

AN:

5168

South Asian (SAS)

AF:

0.150

AC:

724

AN:

4826

European-Finnish (FIN)

AF:

0.0866

AC:

917

AN:

10594

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.108

AC:

7317

AN:

67964

Other (OTH)

AF:

0.132

AC:

280

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

924

1847

2771

3694

4618

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

234

468

702

936

1170

<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:

0.119

Hom.:

4403

Bravo

AF:

0.144

Asia WGS

AF:

0.212

AC:

737

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

7.4

(source)

DANN

Benign

0.26

PhyloP100

1.0

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