15-83783300-T-C

Variant names:

• chr15-83783300-T-C
• rs1426165
• NM_207517.3:c.317+9650T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_207517.3(ADAMTSL3):​c.317+9650T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,480 control chromosomes in the GnomAD database, including 13,139 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 0.40 (13139 hom., cov: 31)
• Consequence: ADAMTSL3 NM_207517.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.994
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.61 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.317+9650T>C		intron	N/A	NP_997400.2
	ADAMTSL3	NM_001301110.2		c.317+9650T>C		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.317+9650T>C		intron	N/A	ENSP00000286744.5
	ADAMTSL3	ENST00000567476.1	TSL:1	c.317+9650T>C		intron	N/A	ENSP00000456313.1
	ADAMTSL3	ENST00000561483.5	TSL:5	n.532+9650T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61158 AN: 151364 Hom.: 13124 Cov.: 31

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.404 AC: 61213 AN: 151480 Hom.: 13139 Cov.: 31 AF XY: 0.410 AC XY: 30356 AN XY: 73996

African (AFR) AF: 0.526 AC: 21731 AN: 41338

American (AMR) AF: 0.396 AC: 6004 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1438 AN: 3468

East Asian (EAS) AF: 0.480 AC: 2474 AN: 5152

South Asian (SAS) AF: 0.628 AC: 3022 AN: 4810

European-Finnish (FIN) AF: 0.313 AC: 3249 AN: 10372

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22028 AN: 67848

Other (OTH) AF: 0.386 AC: 814 AN: 2108

Alfa AF: 0.357 Hom.: 5461

Bravo AF: 0.410

Asia WGS AF: 0.537 AC: 1851 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.58
PhyloP100		0.99
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: rs1426165; hg19: chr15-84452052;