Variant 15-83704567-C-CAG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.315

Variant links:

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]

ADAMTSL3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Protein	UniProt
ADAMTSL3	NM_207517.3 link	c.189+59_189+60insAG		intron_variant		ENST00000286744.10	NP_997400.2	P82987-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAMTSL3	ENST00000286744.10 link	c.189+59_189+60insAG		intron_variant		1	NM_207517.3	ENSP00000286744.5		P82987-1

Frequencies

GnomAD3 genomes

AF:

0.840

AC:

127636

AN:

151868

Hom.:

54112

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.843

AC XY:

62616

AN XY:

74286

show subpopulations

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

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over