15-83913152-T-G

Variant names:

• chr15-83913152-T-G
• rs4842923
• NM_207517.3:c.1761T>G

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_207517.3(ADAMTSL3):​c.1761T>G​(p.Arg587Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. R587R) has been classified as Benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: ADAMTSL3 NM_207517.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.18
• Publications: 26 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: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP7: Synonymous conserved (PhyloP=-5.18 with no splicing effect.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTSL3	NM_207517.3	MANE Select	c.1761T>G	p.Arg587Arg	synonymous	Exon 16 of 30	NP_997400.2
	ADAMTSL3	NM_001301110.2		c.1761T>G	p.Arg587Arg	synonymous	Exon 16 of 30	NP_001288039.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTSL3	ENST00000286744.10	TSL:1 MANE Select	c.1761T>G	p.Arg587Arg	synonymous	Exon 16 of 30	ENSP00000286744.5
	ADAMTSL3	ENST00000567476.1	TSL:1	c.1761T>G	p.Arg587Arg	synonymous	Exon 16 of 30	ENSP00000456313.1
	ADAMTSL3	ENST00000963409.1		c.1761T>G	p.Arg587Arg	synonymous	Exon 16 of 30	ENSP00000633468.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 66

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 45274

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.75
DANN	Benign	0.46
PhyloP100		-5.2

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: rs4842923; hg19: chr15-84581904;