rs922693

Variant names:

• chr15-78807196-G-A
• rs922693
• NM_014272.5:c.100+3925C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-78807196-G-A
• chr15-78807196-G-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The NM_014272.5(ADAMTS7):​c.100+3925C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 152,108 control chromosomes in the GnomAD database, including 37,856 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency: Genomes: 𝑓 0.70 (37856 hom., cov: 33)
• Consequence: ADAMTS7 NM_014272.5 intron
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.0230

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP6: Variant 15-78807196-G-A is Benign according to our data. Variant chr15-78807196-G-A is described in ClinVar as [Benign]. Clinvar id is 812636.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTS7	NM_014272.5	c.100+3925C>T		intron_variant	Intron 1 of 23	ENST00000388820.5	NP_055087.2
ADAMTS7	XM_047432122.1	c.100+3925C>T		intron_variant	Intron 1 of 23		XP_047288078.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMTS7	ENST00000388820.5	c.100+3925C>T		intron_variant	Intron 1 of 23	1	NM_014272.5	ENSP00000373472.4
ADAMTS7	ENST00000566303.5	n.163+3925C>T		intron_variant	Intron 1 of 9	5
ADAMTS7	ENST00000568712.1	n.112+3925C>T		intron_variant	Intron 1 of 14	2

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106838 AN: 151990 Hom.: 37833 Cov.: 33

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.703 AC: 106904 AN: 152108 Hom.: 37856 Cov.: 33 AF XY: 0.700 AC XY: 52030 AN XY: 74360

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.741

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.738

Alfa AF: 0.705 Hom.: 7656

Bravo AF: 0.698

Asia WGS AF: 0.653 AC: 2272 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

Three Vessel Coronary Disease Benign:1

-

Department of Cardiology, Chinese Academy of Medical Sciences, Fuwai Hospital

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.76
DANN	Benign	0.55

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: rs922693; hg19: chr15-79099538;