NM_014272.5:c.100+3925C>T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014272.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS7	NM_014272.5	MANE Select	c.100+3925C>T		intron	N/A	NP_055087.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS7	ENST00000388820.5	TSL:1 MANE Select	c.100+3925C>T		intron	N/A	ENSP00000373472.4
	ADAMTS7	ENST00000972106.1		c.100+3925C>T		intron	N/A	ENSP00000642165.1
	ADAMTS7	ENST00000972107.1		c.100+3925C>T		intron	N/A	ENSP00000642166.1

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

African (AFR) AF: 0.649 AC: 26925 AN: 41462

American (AMR) AF: 0.703 AC: 10752 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2777 AN: 3472

East Asian (EAS) AF: 0.489 AC: 2523 AN: 5160

South Asian (SAS) AF: 0.741 AC: 3577 AN: 4826

European-Finnish (FIN) AF: 0.736 AC: 7788 AN: 10586

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.738 AC: 50151 AN: 67996

Other (OTH) AF: 0.738 AC: 1561 AN: 2114

Alfa AF: 0.696 Hom.: 17134

Bravo AF: 0.698

Asia WGS AF: 0.653 AC: 2272 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	Three Vessel Coronary Disease (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.76
DANN	Benign	0.55
PhyloP100		-0.023
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs922693; hg19: chr15-79099538;