rs11259933

Positions:

• chr15-83911404-G-A
• chr15-83911404-G-C

Variant summary

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

The NM_207517.3(ADAMTSL3):​c.1701-1688G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 152,108 control chromosomes in the GnomAD database, including 31,024 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 0.63 (31024 hom., cov: 33)
• Consequence: ADAMTSL3 NM_207517.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTSL3	NM_207517.3	c.1701-1688G>A		intron_variant		ENST00000286744.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAMTSL3	ENST00000286744.10	c.1701-1688G>A		intron_variant		1	NM_207517.3	P1
ADAMTSL3	ENST00000567476.1	c.1701-1688G>A		intron_variant		1
ADAMTSL3	ENST00000561483.5	n.1916-1688G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95311 AN: 151990 Hom.: 30976 Cov.: 33

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.627 AC: 95421 AN: 152108 Hom.: 31024 Cov.: 33 AF XY: 0.629 AC XY: 46746 AN XY: 74364

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.616

Alfa AF: 0.595 Hom.: 4837

Bravo AF: 0.650

Asia WGS AF: 0.674 AC: 2343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.73

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: rs11259933; hg19: chr15-84580156;