Variant chr15-83655689-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_207517.3(ADAMTSL3):c.-33-40G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 1,455,024 control chromosomes in the GnomAD database, including 45,692 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 4067 hom., cov: 32)

Exomes 𝑓: 0.24 ( 41625 hom. )

Consequence

ADAMTSL3
NM_207517.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0170

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 15-83655689-G-A is Benign according to our data. Variant chr15-83655689-G-A is described in ClinVar as [Benign]. Clinvar id is 1258788.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAMTSL3	NM_207517.3 link	c.-33-40G>A		intron_variant		ENST00000286744.10	NP_997400.2	P82987-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
ADAMTSL3	ENST00000286744.10 link	c.-33-40G>A	intron_variant	1	NM_207517.3	ENSP00000286744.5	P82987-1
ADAMTSL3	ENST00000567476.1 link	c.-33-40G>A	intron_variant	1		ENSP00000456313.1	P82987-2
ADAMTSL3	ENST00000561483.5 link	n.183-40G>A	intron_variant	5
ADAMTSL3	ENST00000569510.5 link	n.183-40G>A	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.202

AC:

30763

AN:

152056

Hom.:

4062

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0497

Gnomad AMI

AF:

0.296

Gnomad AMR

AF:

0.341

Gnomad ASJ

AF:

0.338

Gnomad EAS

AF:

0.0677

Gnomad SAS

AF:

0.135

Gnomad FIN

AF:

0.239

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.263

Gnomad OTH

AF:

0.246

GnomAD4 exome

AF:

0.243

AC:

317232

AN:

1302850

Hom.:

41625

Cov.:

AF XY:

0.241

AC XY:

157837

AN XY:

653948

show subpopulations

Gnomad4 AFR exome

AF:

0.0397

Gnomad4 AMR exome

AF:

0.384

Gnomad4 ASJ exome

AF:

0.349

Gnomad4 EAS exome

AF:

0.0775

Gnomad4 SAS exome

AF:

0.158

Gnomad4 FIN exome

AF:

0.233

Gnomad4 NFE exome

AF:

0.255

Gnomad4 OTH exome

AF:

0.233

GnomAD4 genome

AF:

0.202

AC:

30769

AN:

152174

Hom.:

4067

Cov.:

AF XY:

0.201

AC XY:

14952

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.0495

Gnomad4 AMR

AF:

0.342

Gnomad4 ASJ

AF:

0.338

Gnomad4 EAS

AF:

0.0681

Gnomad4 SAS

AF:

0.134

Gnomad4 FIN

AF:

0.239

Gnomad4 NFE

AF:

0.263

Gnomad4 OTH

AF:

0.245

Alfa

AF:

0.224

Hom.:

720

Bravo

AF:

0.207

Asia WGS

AF:

0.110

AC:

383

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.2

DANN

Benign

0.60

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over