15-83888924-T-G

Position:

• chr15-83888924-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_207517.3(ADAMTSL3):​c.1073-1185T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 152,088 control chromosomes in the GnomAD database, including 30,955 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.62 (30955 hom., cov: 32)
• Consequence: ADAMTSL3 NM_207517.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.620

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTSL3	NM_207517.3	c.1073-1185T>G		intron_variant		ENST00000286744.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAMTSL3	ENST00000286744.10	c.1073-1185T>G		intron_variant		1	NM_207517.3	P1
ADAMTSL3	ENST00000567476.1	c.1073-1185T>G		intron_variant		1
ADAMTSL3	ENST00000561483.5	n.1288-1185T>G		intron_variant, non_coding_transcript_variant		5
ADAMTSL3	ENST00000567663.1	n.49-1185T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94818 AN: 151970 Hom.: 30906 Cov.: 32

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.624 AC: 94928 AN: 152088 Hom.: 30955 Cov.: 32 AF XY: 0.625 AC XY: 46448 AN XY: 74334

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.702

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.607

Alfa AF: 0.544 Hom.: 12295

Bravo AF: 0.648

Asia WGS AF: 0.676 AC: 2348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.52

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: rs2401171; hg19: chr15-84557676;