Genetic Variant MMP20-AS1:n.234-830T>C (chr11-102625829-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000542119.2(MMP20-AS1):n.234-830T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 152,106 control chromosomes in the GnomAD database, including 28,414 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 0.61 ( 28414 hom., cov: 32)

Consequence

MMP20-AS1
ENST00000542119.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.295

Publications

6 publications found

Variant links:

Genes affected

MMP20-AS1 (HGNC:56362): (MMP20 antisense RNA 1)

MMP20-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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MMP20-AS1	ENST00000542119.2 link	n.234-830T>C		intron_variant	Intron 1 of 3	3
MMP20-AS1	ENST00000782665.1 link	n.590-830T>C		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.611

AC:

92801

AN:

151988

Hom.:

28394

Cov.:

show subpopulations

Gnomad AFR

AF:

0.594

Gnomad AMI

AF:

0.745

Gnomad AMR

AF:

0.577

Gnomad ASJ

AF:

0.599

Gnomad EAS

AF:

0.500

Gnomad SAS

AF:

0.550

Gnomad FIN

AF:

0.686

Gnomad MID

AF:

0.528

Gnomad NFE

AF:

0.628

Gnomad OTH

AF:

0.613

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

GnomAD4 genome

AF:

0.610

AC:

92858

AN:

152106

Hom.:

28414

Cov.:

AF XY:

0.611

AC XY:

45438

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.594

AC:

24660

AN:

41488

American (AMR)

AF:

0.576

AC:

8812

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.599

AC:

2079

AN:

3470

East Asian (EAS)

AF:

0.500

AC:

2584

AN:

5172

South Asian (SAS)

AF:

0.549

AC:

2643

AN:

4814

European-Finnish (FIN)

AF:

0.686

AC:

7265

AN:

10592

Middle Eastern (MID)

AF:

0.524

AC:

154

AN:

294

European-Non Finnish (NFE)

AF:

0.628

AC:

42701

AN:

67962

Other (OTH)

AF:

0.605

AC:

1281

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1878

3756

5634

7512

9390

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

774

1548

2322

3096

3870

<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:

0.612

Hom.:

33635

Bravo

AF:

0.607

Asia WGS

AF:

0.521

AC:

1813

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.5

(source)

DANN

Benign

0.58

PhyloP100

-0.29

PromoterAI

0.0060

Neutral

(source)

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over