dbSNP rs6060269: MMP24-AS1-EDEM2:c.-16-1777G>T (chr20-35148712-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001355008.2(MMP24-AS1-EDEM2):c.-16-1777G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.17 ( 385 hom., cov: 0)

Consequence

MMP24-AS1-EDEM2
NM_001355008.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.866

Publications

4 publications found

Variant links:

Genes affected

MMP24-AS1-EDEM2 (HGNC:):

MMP24-AS1-EDEM2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001355008.2. 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
	MMP24-AS1-EDEM2	NM_001355008.2		c.-16-1777G>T		intron	N/A	NP_001341937.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes

AF:

0.169

AC:

3295

AN:

19448

Hom.:

380

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0881

Gnomad AMI

AF:

0.0984

Gnomad AMR

AF:

0.174

Gnomad ASJ

AF:

0.151

Gnomad EAS

AF:

0.149

Gnomad SAS

AF:

0.226

Gnomad FIN

AF:

0.451

Gnomad MID

AF:

0.281

Gnomad NFE

AF:

0.200

Gnomad OTH

AF:

0.205

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

GnomAD4 genome

AF:

0.170

AC:

3319

AN:

19494

Hom.:

385

Cov.:

AF XY:

0.188

AC XY:

1770

AN XY:

9408

show subpopulations

African (AFR)

AF:

0.0897

AC:

624

AN:

6956

American (AMR)

AF:

0.174

AC:

238

AN:

1370

Ashkenazi Jewish (ASJ)

AF:

0.151

AC:

AN:

504

East Asian (EAS)

AF:

0.151

AC:

AN:

558

South Asian (SAS)

AF:

0.226

AC:

AN:

394

European-Finnish (FIN)

AF:

0.451

AC:

479

AN:

1062

Middle Eastern (MID)

AF:

0.313

AC:

AN:

European-Non Finnish (NFE)

AF:

0.200

AC:

1650

AN:

8234

Other (OTH)

AF:

0.218

AC:

AN:

262

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

108

216

325

433

541

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

168

210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.10

(source)

DANN

Benign

0.64

PhyloP100

-0.87

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over