rs8030379

Variant names:

• chr15-83922158-G-A
• rs8030379
• NM_207517.3:c.1988-1746G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-83922158-G-A
• chr15-83922158-G-C
• chr15-83922158-G-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.1988-1746G>A 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 151,962 control chromosomes in the GnomAD database, including 31,002 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 (31002 hom., cov: 32)
• Consequence: ADAMTSL3 NM_207517.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.674
• Publications: 11 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTSL3	NM_207517.3	c.1988-1746G>A		intron_variant	Intron 16 of 29	ENST00000286744.10	NP_997400.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMTSL3	ENST00000286744.10	c.1988-1746G>A		intron_variant	Intron 16 of 29	1	NM_207517.3	ENSP00000286744.5
ADAMTSL3	ENST00000567476.1	c.1988-1746G>A		intron_variant	Intron 16 of 29	1		ENSP00000456313.1
ADAMTSL3	ENST00000561483.5	n.2203-1746G>A		intron_variant	Intron 16 of 26	5

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95235 AN: 151844 Hom.: 30954 Cov.: 32

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.668

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: 95345 AN: 151962 Hom.: 31002 Cov.: 32 AF XY: 0.629 AC XY: 46679 AN XY: 74242

African (AFR) AF: 0.787 AC: 32652 AN: 41484

American (AMR) AF: 0.708 AC: 10810 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2142 AN: 3468

East Asian (EAS) AF: 0.745 AC: 3853 AN: 5172

South Asian (SAS) AF: 0.614 AC: 2956 AN: 4816

European-Finnish (FIN) AF: 0.513 AC: 5393 AN: 10508

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35517 AN: 67936

Other (OTH) AF: 0.616 AC: 1299 AN: 2108

Alfa AF: 0.654 Hom.: 6718

Bravo AF: 0.650

Asia WGS AF: 0.674 AC: 2333 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.26
PhyloP100		0.67
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: rs8030379; hg19: chr15-84590910;