Genetic Variant ADAMTSL3:c.364-132delA (chr15-83819661-CA-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_207517.3(ADAMTSL3):c.364-132delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 521,626 control chromosomes in the GnomAD database, including 30,212 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.73 ( 29994 hom., cov: 0)

Exomes 𝑓: 0.40 ( 218 hom. )

Consequence

ADAMTSL3
NM_207517.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.436

Publications

0 publications found

Variant links:

Genes affected

ADAMTSL3 (HGNC:14633): (ADAMTS like 3) Predicted to be involved in extracellular matrix organization. Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

ADAMTSL3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 15-83819661-CA-C is Benign according to our data. Variant chr15-83819661-CA-C is described in ClinVar as Benign. ClinVar VariationId is 1279714.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207517.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTSL3	NM_207517.3	MANE Select	c.364-132delA		intron	N/A	NP_997400.2	P82987-1
	ADAMTSL3	NM_001301110.2		c.364-132delA		intron	N/A	NP_001288039.1	P82987-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADAMTSL3	ENST00000286744.10	TSL:1 MANE Select	c.364-149delA	intron	N/A	ENSP00000286744.5	P82987-1
ADAMTSL3	ENST00000567476.1	TSL:1	c.364-149delA	intron	N/A	ENSP00000456313.1	P82987-2
ADAMTSL3	ENST00000963409.1		c.364-149delA	intron	N/A	ENSP00000633468.1

Frequencies

GnomAD3 genomes

AF:

0.729

AC:

87842

AN:

120474

Hom.:

30009

Cov.:

show subpopulations

Gnomad AFR

AF:

0.689

Gnomad AMI

AF:

0.802

Gnomad AMR

AF:

0.784

Gnomad ASJ

AF:

0.742

Gnomad EAS

AF:

0.953

Gnomad SAS

AF:

0.903

Gnomad FIN

AF:

0.688

Gnomad MID

AF:

0.769

Gnomad NFE

AF:

0.715

Gnomad OTH

AF:

0.729

GnomAD4 exome

AF:

0.402

AC:

161197

AN:

401198

Hom.:

218

AF XY:

0.403

AC XY:

84717

AN XY:

210212

show subpopulations

African (AFR)

AF:

0.381

AC:

4328

AN:

11346

American (AMR)

AF:

0.414

AC:

7189

AN:

17356

Ashkenazi Jewish (ASJ)

AF:

0.396

AC:

4858

AN:

12282

East Asian (EAS)

AF:

0.466

AC:

13376

AN:

28674

South Asian (SAS)

AF:

0.422

AC:

15728

AN:

37266

European-Finnish (FIN)

AF:

0.388

AC:

10603

AN:

27318

Middle Eastern (MID)

AF:

0.410

AC:

724

AN:

1764

European-Non Finnish (NFE)

AF:

0.393

AC:

94948

AN:

241904

Other (OTH)

AF:

0.405

AC:

9443

AN:

23288

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.407

Heterozygous variant carriers

6248

12496

18743

24991

31239

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

748

1496

2244

2992

3740

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.729

AC:

87802

AN:

120428

Hom.:

29994

Cov.:

AF XY:

0.733

AC XY:

41875

AN XY:

57156

show subpopulations

African (AFR)

AF:

0.689

AC:

22085

AN:

32074

American (AMR)

AF:

0.784

AC:

9536

AN:

12164

Ashkenazi Jewish (ASJ)

AF:

0.742

AC:

2196

AN:

2960

East Asian (EAS)

AF:

0.953

AC:

4036

AN:

4234

South Asian (SAS)

AF:

0.904

AC:

3190

AN:

3530

European-Finnish (FIN)

AF:

0.688

AC:

4076

AN:

5924

Middle Eastern (MID)

AF:

0.759

AC:

176

AN:

232

European-Non Finnish (NFE)

AF:

0.715

AC:

40684

AN:

56894

Other (OTH)

AF:

0.732

AC:

1199

AN:

1638

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1107

2214

3321

4428

5535

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

690

1380

2070

2760

3450

<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:

0.00

Hom.:

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.44

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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15-83819661-CAAAAAAA-CAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over