15-83819661-CAAAAAAA-CAAAAAAAAA

Variant names:

• chr15-83819661-C-CAA
• rs11301352
• NM_207517.3:c.364-133_364-132dupAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_207517.3(ADAMTSL3):​c.364-133_364-132dupAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000235 in 523,708 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 0.000017 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00030 (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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTSL3	NM_207517.3	c.364-133_364-132dupAA		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.364-150_364-149insAA		intron_variant	Intron 5 of 29	1	NM_207517.3	ENSP00000286744.5

Frequencies

GnomAD3 genomes AF: 0.0000166 AC: 2 AN: 120480 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000312

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000176

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000300 AC: 121 AN: 403228 Hom.: 0 AF XY: 0.000298 AC XY: 63 AN XY: 211312

Gnomad4 AFR exome AF: 0.000526

Gnomad4 AMR exome AF: 0.000172

Gnomad4 ASJ exome AF: 0.000324

Gnomad4 EAS exome AF: 0.0000347

Gnomad4 SAS exome AF: 0.000267

Gnomad4 FIN exome AF: 0.000291

Gnomad4 NFE exome AF: 0.000354

Gnomad4 OTH exome AF: 0.0000428

GnomAD4 genome AF: 0.0000166 AC: 2 AN: 120480 Hom.: 0 Cov.: 0 AF XY: 0.0000175 AC XY: 1 AN XY: 57150

Gnomad4 AFR AF: 0.0000312

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000176

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;