15-83704567-C-CAG

Variant names:

• chr15-83704567-C-CAG
• rs3079595
• NM_207517.3:c.189+59_189+60insAG

Variant summary

Our verdict is Benign. The variant received -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
• 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 -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 rank	MANE	Protein	UniProt
ADAMTSL3	NM_207517.3	c.189+59_189+60insAG		intron_variant	Intron 3 of 29	ENST00000286744.10	NP_997400.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMTSL3	ENST00000286744.10	c.189+59_189+60insAG		intron_variant	Intron 3 of 29	1	NM_207517.3	ENSP00000286744.5

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

African (AFR) AF: 0.942 AC: 31023 AN: 32948

American (AMR) AF: 0.870 AC: 37730 AN: 43378

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 21790 AN: 25644

East Asian (EAS) AF: 0.959 AC: 37940 AN: 39582

South Asian (SAS) AF: 0.931 AC: 78982 AN: 84874

European-Finnish (FIN) AF: 0.752 AC: 40038 AN: 53276

Middle Eastern (MID) AF: 0.848 AC: 4835 AN: 5702

European-Non Finnish (NFE) AF: 0.775 AC: 857095 AN: 1105422

Other (OTH) AF: 0.812 AC: 48628 AN: 59850

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

African (AFR) AF: 0.935 AC: 38802 AN: 41500

American (AMR) AF: 0.851 AC: 13012 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 3003 AN: 3470

East Asian (EAS) AF: 0.961 AC: 4974 AN: 5174

South Asian (SAS) AF: 0.939 AC: 4522 AN: 4816

European-Finnish (FIN) AF: 0.748 AC: 7865 AN: 10520

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52782 AN: 67912

Other (OTH) AF: 0.836 AC: 1762 AN: 2108

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

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.32
Mutation Taster		=19/81	disease causing

Splicing

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

Other links and lift over

dbSNP: rs3079595; hg19: chr15-84373319;