15-83704618-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_207517.3(ADAMTSL3):c.189+110G>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 1,433,164 control chromosomes in the GnomAD database, including 44,360 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.20 (3965 hom., cov: 33)
  • Exomes 𝑓: 0.24 (40395 hom.)
• Consequence: ADAMTSL3 NM_207517.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0200

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 15-83704618-G-A is Benign according to our data. Variant chr15-83704618-G-A is described in ClinVar as [Benign]. Clinvar id is 1279078.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTSL3	NM_207517.3	c.189+110G>A		intron_variant		ENST00000286744.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAMTSL3	ENST00000286744.10	c.189+110G>A		intron_variant		1	NM_207517.3	P1

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30332 AN: 152036 Hom.: 3960 Cov.: 33

Gnomad AFR AF: 0.0481

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.0722

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.248

GnomAD4 exome AF: 0.244 AC: 312291 AN: 1281010 Hom.: 40395 AF XY: 0.242 AC XY: 153906 AN XY: 635620

Gnomad4 AFR exome AF: 0.0392

Gnomad4 AMR exome AF: 0.361

Gnomad4 ASJ exome AF: 0.334

Gnomad4 EAS exome AF: 0.0781

Gnomad4 SAS exome AF: 0.170

Gnomad4 FIN exome AF: 0.198

Gnomad4 NFE exome AF: 0.258

Gnomad4 OTH exome AF: 0.236

GnomAD4 genome AF: 0.199 AC: 30339 AN: 152154 Hom.: 3965 Cov.: 33 AF XY: 0.198 AC XY: 14705 AN XY: 74384

Gnomad4 AFR AF: 0.0479

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.0724

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.247

Alfa AF: 0.239 Hom.: 886

Bravo AF: 0.206

Asia WGS AF: 0.127 AC: 442 AN: 3478

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

Nov 10, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.1
Dann	Benign	0.41

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: rs890309; hg19: chr15-84373370;