rs1340044

Variant names:

• chr9-18362107-T-A
• rs1340044
• ENST00000680146.1:c.208-142722T>A

Your query was ambiguous. Multiple possible variants found:

• chr9-18362107-T-A
• chr9-18362107-T-G

Variant summary

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

The ENST00000680146.1(ADAMTSL1):​c.208-142722T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,908 control chromosomes in the GnomAD database, including 20,983 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 0.52 (20980 hom., cov: 32)
  • Exomes 𝑓: 0.80 (3 hom.)
• Consequence: ADAMTSL1 ENST00000680146.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

ADAMTSL1 (HGNC:14632): (ADAMTS like 1) This gene encodes a secreted protein and member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motif) family. This protein lacks the metalloproteinase and disintegrin-like domains, which are typical of the ADAMTS family, but contains other ADAMTS domains, including the thrombospondin type 1 motif. This protein may have important functions in the extracellular matrix. Alternative splicing results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Jul 2008]

ENSG00000227167 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTSL1	XM_011518063.3	c.262-142722T>A		intron_variant	Intron 3 of 30		XP_011516365.1
ADAMTSL1	XM_017015310.2	c.220-142722T>A		intron_variant	Intron 2 of 29		XP_016870799.1
ADAMTSL1	XM_011518064.4	c.217-142722T>A		intron_variant	Intron 2 of 29		XP_011516366.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMTSL1	ENST00000680146.1	c.208-142722T>A		intron_variant	Intron 2 of 29			ENSP00000505591.1
ENSG00000227167	ENST00000443359.1	n.114A>T		non_coding_transcript_exon_variant	Exon 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79617 AN: 151780 Hom.: 20963 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.510

GnomAD4 exome AF: 0.800 AC: 8 AN: 10 Hom.: 3 Cov.: 0 AF XY: 0.800 AC XY: 8 AN XY: 10

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.524 AC: 79668 AN: 151898 Hom.: 20980 Cov.: 32 AF XY: 0.520 AC XY: 38579 AN XY: 74230

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.512

Alfa AF: 0.520 Hom.: 2551

Bravo AF: 0.518

Asia WGS AF: 0.518 AC: 1802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.15
DANN	Benign	0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1340044; hg19: chr9-18362105;