15-83804411-T-C

Variant names:

• chr15-83804411-T-C
• rs11856213
• NM_207517.3:c.318-239T>C

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.318-239T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,958 control chromosomes in the GnomAD database, including 6,388 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.28 (6388 hom., cov: 31)
• Consequence: ADAMTSL3 NM_207517.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.53
• Publications: 1 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=-0.83).
• BP6: Variant 15-83804411-T-C is Benign according to our data. Variant chr15-83804411-T-C is described in ClinVar as Benign. ClinVar VariationId is 1181047.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.547 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.318-239T>C		intron	N/A	NP_997400.2	P82987-1
	ADAMTSL3	NM_001301110.2		c.318-239T>C		intron	N/A	NP_001288039.1	P82987-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTSL3	ENST00000286744.10	TSL:1 MANE Select	c.318-239T>C		intron	N/A	ENSP00000286744.5	P82987-1
	ADAMTSL3	ENST00000567476.1	TSL:1	c.318-239T>C		intron	N/A	ENSP00000456313.1	P82987-2
	ADAMTSL3	ENST00000963409.1		c.318-239T>C		intron	N/A	ENSP00000633468.1

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43096 AN: 151838 Hom.: 6383 Cov.: 31

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.284 AC: 43123 AN: 151958 Hom.: 6388 Cov.: 31 AF XY: 0.292 AC XY: 21665 AN XY: 74294

African (AFR) AF: 0.318 AC: 13192 AN: 41432

American (AMR) AF: 0.202 AC: 3090 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1168 AN: 3468

East Asian (EAS) AF: 0.333 AC: 1717 AN: 5162

South Asian (SAS) AF: 0.565 AC: 2708 AN: 4792

European-Finnish (FIN) AF: 0.297 AC: 3136 AN: 10574

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17134 AN: 67952

Other (OTH) AF: 0.277 AC: 585 AN: 2110

Alfa AF: 0.262 Hom.: 16812

Bravo AF: 0.271

Asia WGS AF: 0.458 AC: 1591 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.8
DANN	Benign	0.41
PhyloP100		1.5
Mutation Taster		=99/1	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: rs11856213; hg19: chr15-84473163;