dbSNP rs1004792: MMP25-AS1:n.942C>T (chr16-3044260-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000722320.1(MMP25-AS1):n.942C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 151,808 control chromosomes in the GnomAD database, including 3,638 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 0.21 ( 3638 hom., cov: 31)

Consequence

MMP25-AS1
ENST00000722320.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.612

Publications

11 publications found

Variant links:

Genes affected

MMP25-AS1 (HGNC:51372): (MMP25 antisense RNA 1)

MMP25-AS1 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=-1.0).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MMP25-AS1	ENST00000722320.1 link	n.942C>T	non_coding_transcript_exon_variant	Exon 3 of 3
MMP25-AS1	ENST00000722321.1 link	n.481C>T	non_coding_transcript_exon_variant	Exon 2 of 2
MMP25-AS1	ENST00000576250.6 link	n.1111-5166C>T	intron_variant	Intron 4 of 6	5

Frequencies

GnomAD3 genomes

AF:

0.213

AC:

32331

AN:

151688

Hom.:

3636

Cov.:

show subpopulations

Gnomad AFR

AF:

0.142

Gnomad AMI

AF:

0.247

Gnomad AMR

AF:

0.200

Gnomad ASJ

AF:

0.174

Gnomad EAS

AF:

0.117

Gnomad SAS

AF:

0.243

Gnomad FIN

AF:

0.304

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.252

Gnomad OTH

AF:

0.202

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

GnomAD4 genome

AF:

0.213

AC:

32356

AN:

151808

Hom.:

3638

Cov.:

AF XY:

0.216

AC XY:

16022

AN XY:

74182

show subpopulations

African (AFR)

AF:

0.142

AC:

5896

AN:

41394

American (AMR)

AF:

0.200

AC:

3046

AN:

15230

Ashkenazi Jewish (ASJ)

AF:

0.174

AC:

603

AN:

3466

East Asian (EAS)

AF:

0.117

AC:

603

AN:

5146

South Asian (SAS)

AF:

0.243

AC:

1168

AN:

4806

European-Finnish (FIN)

AF:

0.304

AC:

3197

AN:

10524

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.252

AC:

17130

AN:

67928

Other (OTH)

AF:

0.203

AC:

428

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1283

2566

3850

5133

6416

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

354

708

1062

1416

1770

<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:

0.232

Hom.:

16224

Bravo

AF:

0.198

Asia WGS

AF:

0.183

AC:

636

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.0

(source)

DANN

Benign

0.42

PhyloP100

-0.61

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over