Variant chr15-83897792-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_207517.3(ADAMTSL3):c.1468-66C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 1,490,046 control chromosomes in the GnomAD database, including 47,531 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.27 ( 6075 hom., cov: 32)

Exomes 𝑓: 0.24 ( 41456 hom. )

Consequence

ADAMTSL3
NM_207517.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.106

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP6

Variant 15-83897792-C-T is Benign according to our data. Variant chr15-83897792-C-T is described in ClinVar as [Benign]. Clinvar id is 1265153.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTSL3	NM_207517.3 linkuse as main transcript	c.1468-66C>T		intron_variant		ENST00000286744.10

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
ADAMTSL3	ENST00000286744.10 linkuse as main transcript	c.1468-66C>T	intron_variant	1	NM_207517.3	P1	P82987-1
ADAMTSL3	ENST00000567476.1 linkuse as main transcript	c.1468-66C>T	intron_variant	1			P82987-2
ADAMTSL3	ENST00000561483.5 linkuse as main transcript	n.1683-66C>T	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.270

AC:

40995

AN:

151942

Hom.:

6051

Cov.:

show subpopulations

Gnomad AFR

AF:

0.307

Gnomad AMI

AF:

0.138

Gnomad AMR

AF:

0.431

Gnomad ASJ

AF:

0.290

Gnomad EAS

AF:

0.360

Gnomad SAS

AF:

0.391

Gnomad FIN

AF:

0.202

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.207

Gnomad OTH

AF:

0.268

GnomAD4 exome

AF:

0.239

AC:

319300

AN:

1337986

Hom.:

41456

AF XY:

0.240

AC XY:

157531

AN XY:

656522

show subpopulations

Gnomad4 AFR exome

AF:

0.304

Gnomad4 AMR exome

AF:

0.539

Gnomad4 ASJ exome

AF:

0.275

Gnomad4 EAS exome

AF:

0.360

Gnomad4 SAS exome

AF:

0.371

Gnomad4 FIN exome

AF:

0.203

Gnomad4 NFE exome

AF:

0.216

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.270

AC:

41072

AN:

152060

Hom.:

6075

Cov.:

AF XY:

0.274

AC XY:

20372

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.308

Gnomad4 AMR

AF:

0.432

Gnomad4 ASJ

AF:

0.290

Gnomad4 EAS

AF:

0.361

Gnomad4 SAS

AF:

0.392

Gnomad4 FIN

AF:

0.202

Gnomad4 NFE

AF:

0.207

Gnomad4 OTH

AF:

0.270

Alfa

AF:

0.231

Hom.:

2061

Bravo

AF:

0.287

Asia WGS

AF:

0.390

AC:

1354

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

BayesDel_noAF

Benign

-0.97

CADD

Benign

5.8

DANN

Benign

0.48

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

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