rs713468

Variant names:

• chr15-83977939-A-G
• rs713468
• NM_207517.3:c.2645-4334A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_207517.3(ADAMTSL3):​c.2645-4334A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,078 control chromosomes in the GnomAD database, including 12,918 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.40 (12918 hom., cov: 33)
• Consequence: ADAMTSL3 NM_207517.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTSL3	NM_207517.3	c.2645-4334A>G		intron_variant	Intron 20 of 29	ENST00000286744.10	NP_997400.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMTSL3	ENST00000286744.10	c.2645-4334A>G		intron_variant	Intron 20 of 29	1	NM_207517.3	ENSP00000286744.5

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60496 AN: 151958 Hom.: 12905 Cov.: 33

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.398 AC: 60546 AN: 152078 Hom.: 12918 Cov.: 33 AF XY: 0.397 AC XY: 29556 AN XY: 74360

African (AFR) AF: 0.562 AC: 23297 AN: 41482

American (AMR) AF: 0.294 AC: 4488 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1257 AN: 3468

East Asian (EAS) AF: 0.376 AC: 1942 AN: 5164

South Asian (SAS) AF: 0.361 AC: 1734 AN: 4808

European-Finnish (FIN) AF: 0.341 AC: 3606 AN: 10572

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22936 AN: 67980

Other (OTH) AF: 0.380 AC: 804 AN: 2114

Alfa AF: 0.354 Hom.: 42263

Bravo AF: 0.402

Asia WGS AF: 0.341 AC: 1187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.80
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs713468; hg19: chr15-84646691;