chr15-83899406-T-A

Variant names:

• chr15-83899406-T-A
• rs10906982
• NM_207517.3:c.1616-241T>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_207517.3(ADAMTSL3):​c.1616-241T>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 151,906 control chromosomes in the GnomAD database, including 30,958 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.63 (30958 hom., cov: 32)
• Consequence: ADAMTSL3 NM_207517.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.135
• Publications: 41 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 15-83899406-T-A is Benign according to our data. Variant chr15-83899406-T-A is described in ClinVar as Benign. ClinVar VariationId is 1261126.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTSL3	NM_207517.3	MANE Select	c.1616-241T>A		intron	N/A	NP_997400.2
	ADAMTSL3	NM_001301110.2		c.1616-241T>A		intron	N/A	NP_001288039.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTSL3	ENST00000286744.10	TSL:1 MANE Select	c.1616-241T>A		intron	N/A	ENSP00000286744.5
	ADAMTSL3	ENST00000567476.1	TSL:1	c.1616-241T>A		intron	N/A	ENSP00000456313.1
	ADAMTSL3	ENST00000561483.5	TSL:5	n.1831-241T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95168 AN: 151786 Hom.: 30910 Cov.: 32

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.627 AC: 95279 AN: 151906 Hom.: 30958 Cov.: 32 AF XY: 0.628 AC XY: 46624 AN XY: 74234

African (AFR) AF: 0.788 AC: 32625 AN: 41418

American (AMR) AF: 0.708 AC: 10812 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2135 AN: 3470

East Asian (EAS) AF: 0.743 AC: 3846 AN: 5174

South Asian (SAS) AF: 0.612 AC: 2938 AN: 4802

European-Finnish (FIN) AF: 0.511 AC: 5385 AN: 10534

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.523 AC: 35518 AN: 67924

Other (OTH) AF: 0.617 AC: 1300 AN: 2106

Alfa AF: 0.429 Hom.: 1158

Bravo AF: 0.650

Asia WGS AF: 0.672 AC: 2331 AN: 3472

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 18, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.65
PhyloP100		-0.14
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: rs10906982; hg19: chr15-84568158;