15-83819661-CAAAAAAA-CAAAA

Variant names:

• chr15-83819661-CAAA-C
• rs11301352
• NM_207517.3:c.364-134_364-132delAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_207517.3(ADAMTSL3):​c.364-134_364-132delAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.055 in 490,962 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00056 (0 hom., cov: 0)
  • Exomes 𝑓: 0.073 (0 hom.)
• Consequence: ADAMTSL3 NM_207517.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436

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 -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTSL3	NM_207517.3	c.364-134_364-132delAAA		intron_variant	Intron 5 of 29	ENST00000286744.10	NP_997400.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMTSL3	ENST00000286744.10	c.364-149_364-147delAAA		intron_variant	Intron 5 of 29	1	NM_207517.3	ENSP00000286744.5

Frequencies

GnomAD3 genomes AF: 0.000556 AC: 67 AN: 120432 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000125

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000494

Gnomad ASJ AF: 0.000338

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00271

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000703

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0727 AC: 26928 AN: 370576 Hom.: 0 AF XY: 0.0738 AC XY: 14337 AN XY: 194252

Gnomad4 AFR exome AF: 0.0471

Gnomad4 AMR exome AF: 0.0743

Gnomad4 ASJ exome AF: 0.0648

Gnomad4 EAS exome AF: 0.0844

Gnomad4 SAS exome AF: 0.111

Gnomad4 FIN exome AF: 0.0644

Gnomad4 NFE exome AF: 0.0681

Gnomad4 OTH exome AF: 0.0713

GnomAD4 genome AF: 0.000557 AC: 67 AN: 120386 Hom.: 0 Cov.: 0 AF XY: 0.000700 AC XY: 40 AN XY: 57128

Gnomad4 AFR AF: 0.000125

Gnomad4 AMR AF: 0.000494

Gnomad4 ASJ AF: 0.000338

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00271

Gnomad4 NFE AF: 0.000703

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs11301352; hg19: chr15-84488413;