Genetic Variant ADAMTSL3:c.364-133_364-132delAA (chr15-83819661-CAA-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_207517.3(ADAMTSL3):c.364-133_364-132delAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 501,936 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0033 ( 1 hom., cov: 0)

Exomes 𝑓: 0.22 ( 0 hom. )

Consequence

ADAMTSL3
NM_207517.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.436

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 made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTSL3	NM_207517.3 link	c.364-133_364-132delAA		intron_variant	Intron 5 of 29	ENST00000286744.10	NP_997400.2	P82987-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMTSL3	ENST00000286744.10 link	c.364-149_364-148delAA		intron_variant	Intron 5 of 29	1	NM_207517.3	ENSP00000286744.5		P82987-1

Frequencies

GnomAD3 genomes

AF:

0.00331

AC:

399

AN:

120406

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00144

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00272

Gnomad ASJ

AF:

0.00101

Gnomad EAS

AF:

0.0226

Gnomad SAS

AF:

0.00592

Gnomad FIN

AF:

0.0108

Gnomad MID

AF:

0.00769

Gnomad NFE

AF:

0.00229

Gnomad OTH

AF:

0.00244

GnomAD4 exome

AF:

0.217

AC:

82788

AN:

381576

Hom.:

AF XY:

0.218

AC XY:

43582

AN XY:

200146

show subpopulations

Gnomad4 AFR exome

AF:

0.206

Gnomad4 AMR exome

AF:

0.228

Gnomad4 ASJ exome

AF:

0.210

Gnomad4 EAS exome

AF:

0.275

Gnomad4 SAS exome

AF:

0.238

Gnomad4 FIN exome

AF:

0.201

Gnomad4 NFE exome

AF:

0.209

Gnomad4 OTH exome

AF:

0.213

GnomAD4 genome

AF:

0.00331

AC:

398

AN:

120360

Hom.:

Cov.:

AF XY:

0.00371

AC XY:

212

AN XY:

57100

show subpopulations

Gnomad4 AFR

AF:

0.00143

Gnomad4 AMR

AF:

0.00272

Gnomad4 ASJ

AF:

0.00101

Gnomad4 EAS

AF:

0.0227

Gnomad4 SAS

AF:

0.00568

Gnomad4 FIN

AF:

0.0108

Gnomad4 NFE

AF:

0.00229

Gnomad4 OTH

AF:

0.00244

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

15-83819661-CAAAAAAA-CAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over