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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MFAP2	NM_002403.4 link	c.*190A>G		3_prime_UTR_variant	Exon 9 of 9	ENST00000375535.4	NP_002394.1	P55001-1A0A024RA94

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MFAP2	ENST00000375535.4 link	c.*190A>G	3_prime_UTR_variant	Exon 9 of 9	1	NM_002403.4	ENSP00000364685.3	P55001-1
MFAP2	ENST00000490075.5 link	n.2143A>G	non_coding_transcript_exon_variant	Exon 6 of 6	2
MFAP2	ENST00000375534.7 link	c.*190A>G	3_prime_UTR_variant	Exon 8 of 8	2		ENSP00000364684.3	P55001-2

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 v4.3

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over