dbSNP rs1051225: MFAP2:c.*190A>G (chr1-16974730-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 NM_002403.4(MFAP2):c.*190A>G variant causes a 3 prime UTR 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 0.36 ( 636 hom., cov: 3)

Exomes 𝑓: 0.46 ( 24539 hom. )

Failed GnomAD Quality Control

Consequence

MFAP2
NM_002403.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.471

Publications

1 publications found

Variant links:

Genes affected

MFAP2 (HGNC:7033): (microfibril associated protein 2) Microfibrillar-associated protein 2 is a major antigen of elastin-associated microfibrils and a candidate for involvement in the etiology of inherited connective tissue diseases. Four transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]

MFAP2 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_002403.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002403.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MFAP2	NM_002403.4	MANE Select	c.*190A>G	3_prime_UTR	Exon 9 of 9	NP_002394.1	P55001-1
MFAP2	NM_017459.3		c.*190A>G	3_prime_UTR	Exon 9 of 9	NP_059453.1	P55001-1
MFAP2	NM_001135247.2		c.*190A>G	3_prime_UTR	Exon 9 of 9	NP_001128719.1	P55001-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MFAP2	ENST00000375535.4	TSL:1 MANE Select	c.*190A>G	3_prime_UTR	Exon 9 of 9	ENSP00000364685.3	P55001-1
MFAP2	ENST00000930335.1		c.*190A>G	3_prime_UTR	Exon 10 of 10	ENSP00000600394.1
MFAP2	ENST00000930331.1		c.*190A>G	3_prime_UTR	Exon 9 of 9	ENSP00000600390.1

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

2797

AN:

7766

Hom.:

635

Cov.:

show subpopulations

Gnomad AFR

AF:

0.400

Gnomad AMI

AF:

0.400

Gnomad AMR

AF:

0.405

Gnomad ASJ

AF:

0.438

Gnomad EAS

AF:

0.194

Gnomad SAS

AF:

0.375

Gnomad FIN

AF:

0.231

Gnomad MID

AF:

0.235

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.438

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.460

AC:

101741

AN:

221306

Hom.:

24539

Cov.:

AF XY:

0.460

AC XY:

52598

AN XY:

114460

show subpopulations

African (AFR)

AF:

0.489

AC:

3767

AN:

7698

American (AMR)

AF:

0.493

AC:

4425

AN:

8980

Ashkenazi Jewish (ASJ)

AF:

0.486

AC:

3405

AN:

7008

East Asian (EAS)

AF:

0.283

AC:

4082

AN:

14406

South Asian (SAS)

AF:

0.449

AC:

9236

AN:

20560

European-Finnish (FIN)

AF:

0.396

AC:

5032

AN:

12704

Middle Eastern (MID)

AF:

0.488

AC:

489

AN:

1002

European-Non Finnish (NFE)

AF:

0.481

AC:

65218

AN:

135694

Other (OTH)

AF:

0.459

AC:

6087

AN:

13254

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

2558

5115

7673

10230

12788

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

418

836

1254

1672

2090

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.360

AC:

2790

AN:

7746

Hom.:

636

Cov.:

AF XY:

0.358

AC XY:

1286

AN XY:

3590

show subpopulations

African (AFR)

AF:

0.401

AC:

647

AN:

1614

American (AMR)

AF:

0.405

AC:

420

AN:

1036

Ashkenazi Jewish (ASJ)

AF:

0.438

AC:

AN:

130

East Asian (EAS)

AF:

0.193

AC:

146

AN:

758

South Asian (SAS)

AF:

0.370

AC:

211

AN:

570

European-Finnish (FIN)

AF:

0.231

AC:

AN:

316

Middle Eastern (MID)

AF:

0.259

AC:

AN:

European-Non Finnish (NFE)

AF:

0.372

AC:

1151

AN:

3098

Other (OTH)

AF:

0.425

AC:

AN:

146

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

162

242

323

404

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.474

Hom.:

1756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.8

(source)

DANN

Benign

0.37

PhyloP100

-0.47

Mutation Taster

=100/0

polymorphism

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over