5-33636489-G-A

Variant names:

• chr5-33636489-G-A
• rs6868223
• NM_030955.4:c.1888+1088C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030955.4(ADAMTS12):​c.1888+1088C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 152,016 control chromosomes in the GnomAD database, including 22,908 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 0.53 (22908 hom., cov: 32)
• Consequence: ADAMTS12 NM_030955.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 15 publications found

Genes affected

ADAMTS12 (HGNC:14605): (ADAM metallopeptidase with thrombospondin type 1 motif 12) This gene encodes a member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) protein family. Members of the family share several distinct protein modules, including a propeptide region, a metalloproteinase domain, a disintegrin-like domain, and a thrombospondin type 1 (TS-1) motif. Individual members of this family differ in the number of C-terminal TS-1 motifs, and some have unique C-terminal domains. The enzyme encoded by this gene contains eight TS-1 motifs. It may play roles in pulmonary cells during fetal development or in tumor processes through its proteolytic activity or as a molecule potentially involved in regulation of cell adhesion. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030955.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS12	NM_030955.4	MANE Select	c.1888+1088C>T		intron	N/A	NP_112217.2
	ADAMTS12	NM_001324512.2		c.1888+1088C>T		intron	N/A	NP_001311441.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS12	ENST00000504830.6	TSL:1 MANE Select	c.1888+1088C>T		intron	N/A	ENSP00000422554.1
	ADAMTS12	ENST00000352040.7	TSL:1	c.1888+1088C>T		intron	N/A	ENSP00000344847.3
	ADAMTS12	ENST00000504582.5	TSL:5	n.1568+1088C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80749 AN: 151896 Hom.: 22892 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.531 AC: 80793 AN: 152016 Hom.: 22908 Cov.: 32 AF XY: 0.531 AC XY: 39468 AN XY: 74280

African (AFR) AF: 0.315 AC: 13077 AN: 41466

American (AMR) AF: 0.599 AC: 9149 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2219 AN: 3468

East Asian (EAS) AF: 0.608 AC: 3145 AN: 5170

South Asian (SAS) AF: 0.484 AC: 2337 AN: 4824

European-Finnish (FIN) AF: 0.616 AC: 6495 AN: 10550

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42385 AN: 67950

Other (OTH) AF: 0.562 AC: 1182 AN: 2104

Alfa AF: 0.598 Hom.: 100844

Bravo AF: 0.524

Asia WGS AF: 0.518 AC: 1801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.74
DANN	Benign	0.66
PhyloP100		-0.15
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: rs6868223; hg19: chr5-33636594;