15-83904289-T-G

Variant names:

• chr15-83904289-T-G
• rs7183263
• NM_207517.3:c.1700+4558T>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_207517.3(ADAMTSL3):​c.1700+4558T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 151,482 control chromosomes in the GnomAD database, including 30,851 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 0.63 (30851 hom., cov: 29)
• Consequence: ADAMTSL3 NM_207517.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.755
• Publications: 27 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207517.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTSL3	NM_207517.3	MANE Select	c.1700+4558T>G		intron	N/A	NP_997400.2
	ADAMTSL3	NM_001301110.2		c.1700+4558T>G		intron	N/A	NP_001288039.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTSL3	ENST00000286744.10	TSL:1 MANE Select	c.1700+4558T>G		intron	N/A	ENSP00000286744.5
	ADAMTSL3	ENST00000567476.1	TSL:1	c.1700+4558T>G		intron	N/A	ENSP00000456313.1
	ADAMTSL3	ENST00000963409.1		c.1700+4558T>G		intron	N/A	ENSP00000633468.1

Frequencies

GnomAD3 genomes AF: 0.627 AC: 94843 AN: 151364 Hom.: 30803 Cov.: 29

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.627 AC: 94953 AN: 151482 Hom.: 30851 Cov.: 29 AF XY: 0.628 AC XY: 46451 AN XY: 73978

African (AFR) AF: 0.787 AC: 32449 AN: 41242

American (AMR) AF: 0.708 AC: 10777 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2132 AN: 3466

East Asian (EAS) AF: 0.743 AC: 3804 AN: 5118

South Asian (SAS) AF: 0.613 AC: 2932 AN: 4780

European-Finnish (FIN) AF: 0.512 AC: 5379 AN: 10502

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35473 AN: 67868

Other (OTH) AF: 0.615 AC: 1285 AN: 2088

Alfa AF: 0.568 Hom.: 55019

Bravo AF: 0.650

Asia WGS AF: 0.674 AC: 2343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	16
DANN	Benign	0.73
PhyloP100		0.76
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: rs7183263; hg19: chr15-84573041;