Genetic Variant ADD3-AS1:n.593+785A>G (chr10-109951059-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000369655.4(ADD3-AS1):n.593+785A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,138 control chromosomes in the GnomAD database, including 5,658 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 0.24 ( 5658 hom., cov: 32)

Consequence

ADD3-AS1
ENST00000369655.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.23

Publications

5 publications found

Variant links:

Genes affected

ADD3-AS1 (HGNC:48682): (ADD3 antisense RNA 1)

ADD3-AS1 links:

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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=-0.93).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADD3-AS1	NR_038943.1 link	n.462+2697A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ADD3-AS1	ENST00000369655.4 link	n.593+785A>G	intron_variant	Intron 4 of 5	1
ADD3-AS1	ENST00000369657.5 link	n.136+2697A>G	intron_variant	Intron 1 of 2	5
ADD3-AS1	ENST00000625954.4 link	n.471+2697A>G	intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.243

AC:

36998

AN:

152020

Hom.:

5636

Cov.:

show subpopulations

Gnomad AFR

AF:

0.395

Gnomad AMI

AF:

0.0965

Gnomad AMR

AF:

0.157

Gnomad ASJ

AF:

0.213

Gnomad EAS

AF:

0.403

Gnomad SAS

AF:

0.513

Gnomad FIN

AF:

0.146

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.158

Gnomad OTH

AF:

0.232

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

GnomAD4 genome

AF:

0.244

AC:

37070

AN:

152138

Hom.:

5658

Cov.:

AF XY:

0.248

AC XY:

18469

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.396

AC:

16417

AN:

41470

American (AMR)

AF:

0.157

AC:

2396

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.213

AC:

738

AN:

3472

East Asian (EAS)

AF:

0.403

AC:

2087

AN:

5178

South Asian (SAS)

AF:

0.514

AC:

2480

AN:

4822

European-Finnish (FIN)

AF:

0.146

AC:

1550

AN:

10588

Middle Eastern (MID)

AF:

0.248

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.158

AC:

10750

AN:

67988

Other (OTH)

AF:

0.232

AC:

491

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1314

2629

3943

5258

6572

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.203

Hom.:

792

Bravo

AF:

0.243

Asia WGS

AF:

0.454

AC:

1579

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.0

(source)

DANN

Benign

0.68

PhyloP100

-1.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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10-109951059-T-C

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