Genetic Variant ADD3-AS1:n.336-22101G>A (chr10-109975992-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 ENST00000369655.4(ADD3-AS1):n.336-22101G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,984 control chromosomes in the GnomAD database, including 4,602 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 0.22 ( 4602 hom., cov: 32)

Consequence

ADD3-AS1
ENST00000369655.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.16

Publications

48 publications found

Variant links:

Genes affected

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

ADD3-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=-0.79).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADD3-AS1	NR_038943.1 link	n.327-22101G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ADD3-AS1	ENST00000369655.4 link	n.336-22101G>A	intron_variant	Intron 2 of 5	1
ADD3-AS1	ENST00000625954.4 link	n.336-22101G>A	intron_variant	Intron 2 of 4	3
ADD3-AS1	ENST00000627565.2 link	n.453+21457G>A	intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.224

AC:

33999

AN:

151866

Hom.:

4595

Cov.:

show subpopulations

Gnomad AFR

AF:

0.334

Gnomad AMI

AF:

0.0965

Gnomad AMR

AF:

0.148

Gnomad ASJ

AF:

0.211

Gnomad EAS

AF:

0.402

Gnomad SAS

AF:

0.487

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.216

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

GnomAD4 genome

AF:

0.224

AC:

34038

AN:

151984

Hom.:

4602

Cov.:

AF XY:

0.229

AC XY:

17027

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.334

AC:

13842

AN:

41420

American (AMR)

AF:

0.147

AC:

2250

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.211

AC:

731

AN:

3470

East Asian (EAS)

AF:

0.402

AC:

2076

AN:

5162

South Asian (SAS)

AF:

0.488

AC:

2349

AN:

4812

European-Finnish (FIN)

AF:

0.147

AC:

1556

AN:

10550

Middle Eastern (MID)

AF:

0.231

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.156

AC:

10619

AN:

67984

Other (OTH)

AF:

0.218

AC:

459

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1289

2578

3866

5155

6444

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

362

724

1086

1448

1810

<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:

0.186

Hom.:

9467

Bravo

AF:

0.221

Asia WGS

AF:

0.438

AC:

1524

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

0.56

(source)

DANN

Benign

0.74

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