15-83804779-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.363+84G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 1,035,476 control chromosomes in the GnomAD database, including 278,486 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.77 (45770 hom., cov: 31)
  • Exomes 𝑓: 0.72 (232716 hom.)
• Consequence: ADAMTSL3 NM_207517.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.39

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=-0.93).
• BP6: Variant 15-83804779-G-A is Benign according to our data. Variant chr15-83804779-G-A is described in ClinVar as [Benign]. Clinvar id is 1294099.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTSL3	NM_207517.3	c.363+84G>A		intron_variant		ENST00000286744.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAMTSL3	ENST00000286744.10	c.363+84G>A		intron_variant		1	NM_207517.3	P1

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116858 AN: 151926 Hom.: 45715 Cov.: 31

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.750

GnomAD4 exome AF: 0.718 AC: 634740 AN: 883430 Hom.: 232716 AF XY: 0.724 AC XY: 323276 AN XY: 446356

Gnomad4 AFR exome AF: 0.878

Gnomad4 AMR exome AF: 0.808

Gnomad4 ASJ exome AF: 0.724

Gnomad4 EAS exome AF: 0.999

Gnomad4 SAS exome AF: 0.925

Gnomad4 FIN exome AF: 0.683

Gnomad4 NFE exome AF: 0.684

Gnomad4 OTH exome AF: 0.736

GnomAD4 genome AF: 0.769 AC: 116972 AN: 152046 Hom.: 45770 Cov.: 31 AF XY: 0.775 AC XY: 57620 AN XY: 74302

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.936

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.754

Alfa AF: 0.724 Hom.: 16421

Bravo AF: 0.776

Asia WGS AF: 0.962 AC: 3342 AN: 3476

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

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.018
Dann	Benign	0.29

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: rs7179507; hg19: chr15-84473531;