15-83837802-G-GA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_207517.3(ADAMTSL3):c.601-275dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 135,502 control chromosomes in the GnomAD database, including 1,803 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.15 (1803 hom., cov: 27)
• Consequence: ADAMTSL3 NM_207517.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.77

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

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 15-83837802-G-GA is Benign according to our data. Variant chr15-83837802-G-GA is described in ClinVar as [Benign]. Clinvar id is 1285835.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTSL3	NM_207517.3	c.601-275dup		intron_variant		ENST00000286744.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAMTSL3	ENST00000286744.10	c.601-275dup		intron_variant		1	NM_207517.3	P1
ADAMTSL3	ENST00000567476.1	c.601-275dup		intron_variant		1
ADAMTSL3	ENST00000561483.5	n.816-275dup		intron_variant, non_coding_transcript_variant		5
ADAMTSL3	ENST00000569510.5	n.816-275dup		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.149 AC: 20144 AN: 135464 Hom.: 1807 Cov.: 27

Gnomad AFR AF: 0.0363

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0400

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.343

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.149 AC: 20133 AN: 135502 Hom.: 1803 Cov.: 27 AF XY: 0.147 AC XY: 9594 AN XY: 65068

Gnomad4 AFR AF: 0.0363

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.0397

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.180

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs11373772; hg19: chr15-84506554;