rs10520582

Variant names:

• chr15-83684024-A-G
• rs10520582
• NM_207517.3:c.70-20365A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-83684024-A-G
• chr15-83684024-A-T

Variant summary

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

The NM_207517.3(ADAMTSL3):​c.70-20365A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.07 in 152,314 control chromosomes in the GnomAD database, including 582 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 0.070 (582 hom., cov: 33)
• Consequence: ADAMTSL3 NM_207517.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTSL3	NM_207517.3	c.70-20365A>G		intron_variant	Intron 2 of 29	ENST00000286744.10	NP_997400.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMTSL3	ENST00000286744.10	c.70-20365A>G		intron_variant	Intron 2 of 29	1	NM_207517.3	ENSP00000286744.5
ADAMTSL3	ENST00000567476.1	c.70-20365A>G		intron_variant	Intron 2 of 29	1		ENSP00000456313.1
ADAMTSL3	ENST00000561483.5	n.285-20365A>G		intron_variant	Intron 2 of 26	5
ADAMTSL3	ENST00000569510.5	n.285-20365A>G		intron_variant	Intron 2 of 8	2

Frequencies

GnomAD3 genomes AF: 0.0700 AC: 10652 AN: 152196 Hom.: 582 Cov.: 33

Gnomad AFR AF: 0.0208

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.0875

Gnomad FIN AF: 0.0334

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0737

Gnomad OTH AF: 0.0819

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

GnomAD4 genome AF: 0.0700 AC: 10663 AN: 152314 Hom.: 582 Cov.: 33 AF XY: 0.0701 AC XY: 5224 AN XY: 74470

African (AFR) AF: 0.0208 AC: 865 AN: 41582

American (AMR) AF: 0.170 AC: 2604 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3472

East Asian (EAS) AF: 0.177 AC: 920 AN: 5190

South Asian (SAS) AF: 0.0876 AC: 422 AN: 4818

European-Finnish (FIN) AF: 0.0334 AC: 354 AN: 10614

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0737 AC: 5013 AN: 68030

Other (OTH) AF: 0.0834 AC: 176 AN: 2110

Alfa AF: 0.0764 Hom.: 434

Bravo AF: 0.0785

Asia WGS AF: 0.115 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.90
DANN	Benign	0.54
PhyloP100		-0.036
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: rs10520582; hg19: chr15-84352776;