15-83804411-T-C

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.318-239T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,958 control chromosomes in the GnomAD database, including 6,388 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.28 (6388 hom., cov: 31)
• Consequence: ADAMTSL3 NM_207517.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.53

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=-0.83).
• BP6: Variant 15-83804411-T-C is Benign according to our data. Variant chr15-83804411-T-C is described in ClinVar as [Benign]. Clinvar id is 1181047.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTSL3	NM_207517.3	c.318-239T>C		intron_variant		ENST00000286744.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAMTSL3	ENST00000286744.10	c.318-239T>C		intron_variant		1	NM_207517.3	P1

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43096 AN: 151838 Hom.: 6383 Cov.: 31

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.276

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.284 AC: 43123 AN: 151958 Hom.: 6388 Cov.: 31 AF XY: 0.292 AC XY: 21665 AN XY: 74294

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.277

Alfa AF: 0.260 Hom.: 10689

Bravo AF: 0.271

Asia WGS AF: 0.458 AC: 1591 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

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.8
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: rs11856213; hg19: chr15-84473163;