15-83704567-C-CAG

Variant summary

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

The NM_207517.3(ADAMTSL3):c.189+59_189+60insAG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 1,602,662 control chromosomes in the GnomAD database, including 518,900 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.84 (54155 hom., cov: 0)
  • Exomes 𝑓: 0.80 (464745 hom.)
• Consequence: ADAMTSL3 NM_207517.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.315

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 15-83704567-C-CAG is Benign according to our data. Variant chr15-83704567-C-CAG is described in ClinVar as [Benign]. Clinvar id is 1221815.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTSL3	NM_207517.3	c.189+59_189+60insAG		intron_variant		ENST00000286744.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAMTSL3	ENST00000286744.10	c.189+59_189+60insAG		intron_variant		1	NM_207517.3	P1

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127636 AN: 151868 Hom.: 54112 Cov.: 0

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.837

GnomAD4 exome AF: 0.798 AC: 1158061 AN: 1450676 Hom.: 464745 AF XY: 0.801 AC XY: 577670 AN XY: 721142

Gnomad4 AFR exome AF: 0.942

Gnomad4 AMR exome AF: 0.870

Gnomad4 ASJ exome AF: 0.850

Gnomad4 EAS exome AF: 0.959

Gnomad4 SAS exome AF: 0.931

Gnomad4 FIN exome AF: 0.752

Gnomad4 NFE exome AF: 0.775

Gnomad4 OTH exome AF: 0.812

GnomAD4 genome AF: 0.840 AC: 127736 AN: 151986 Hom.: 54155 Cov.: 0 AF XY: 0.843 AC XY: 62616 AN XY: 74286

Gnomad4 AFR AF: 0.935

Gnomad4 AMR AF: 0.851

Gnomad4 ASJ AF: 0.865

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.939

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.836

Alfa AF: 0.801 Hom.: 6015

Bravo AF: 0.846

Asia WGS AF: 0.931 AC: 3238 AN: 3478

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

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3079595; hg19: chr15-84373319;