rs1994016

Positions:

• chr15-78787892-C-T

Variant summary

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

The NM_014272.5(ADAMTS7):​c.1322+339G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,962 control chromosomes in the GnomAD database, including 8,123 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 0.30 (8123 hom., cov: 31)
• Consequence: ADAMTS7 NM_014272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

ADAMTS7 (HGNC:223): (ADAM metallopeptidase with thrombospondin type 1 motif 7) The protein encoded by this gene is a member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) family. Members of this family share several distinct protein modules, including a propeptide region, a metalloproteinase domain, a disintegrin-like domain, and a thrombospondin type 1 (TS) motif. Individual members of this family differ in the number of C-terminal TS motifs, and some have unique C-terminal domains. The encoded preproprotein is proteolytically processed to generate the mature enzyme. This enzyme contains two C-terminal TS motifs and may regulate vascular smooth muscle cell (VSMC) migration. Mutations in this gene may be associated with susceptibility to coronary artery disease. [provided by RefSeq, Feb 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTS7	NM_014272.5	c.1322+339G>A		intron_variant		ENST00000388820.5
ADAMTS7	XM_047432122.1	c.1322+339G>A		intron_variant
ADAMTS7	XM_047432123.1	c.563+339G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAMTS7	ENST00000388820.5	c.1322+339G>A		intron_variant		1	NM_014272.5	P1
ADAMTS7	ENST00000565793.5	n.1219+339G>A		intron_variant, non_coding_transcript_variant		2
ADAMTS7	ENST00000566303.5	n.1309+339G>A		intron_variant, non_coding_transcript_variant		5
ADAMTS7	ENST00000568712.1	n.1334+339G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45875 AN: 151844 Hom.: 8120 Cov.: 31

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.0873

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.302 AC: 45879 AN: 151962 Hom.: 8123 Cov.: 31 AF XY: 0.296 AC XY: 21958 AN XY: 74284

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.0867

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.322

Alfa AF: 0.376 Hom.: 5149

Bravo AF: 0.292

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.69

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: rs1994016; hg19: chr15-79080234;