15-83819661-CA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_207517.3(ADAMTSL3):c.364-132del 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.436

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]

ACMG classification

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTSL3	NM_207517.3	c.364-132del		intron_variant		ENST00000286744.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAMTSL3	ENST00000286744.10	c.364-132del		intron_variant		1	NM_207517.3	P1

Frequencies

GnomAD3 genomes AF: 0.729 AC: 87842 AN: 120474 Hom.: 30009 Cov.: 0

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

Gnomad4 AFR exome AF: 0.381

Gnomad4 AMR exome AF: 0.414

Gnomad4 ASJ exome AF: 0.396

Gnomad4 EAS exome AF: 0.466

Gnomad4 SAS exome AF: 0.422

Gnomad4 FIN exome AF: 0.388

Gnomad4 NFE exome AF: 0.393

Gnomad4 OTH exome AF: 0.405

GnomAD4 genome AF: 0.729 AC: 87802 AN: 120428 Hom.: 29994 Cov.: 0 AF XY: 0.733 AC XY: 41875 AN XY: 57156

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.742

Gnomad4 EAS AF: 0.953

Gnomad4 SAS AF: 0.904

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.732

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs11301352; hg19: chr15-84488413;