GeneBe

5-154106266-T-C

Variant names:

Variant summary

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

The ENST00000518497.6(MFAP3):​n.249+8995T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,996 control chromosomes in the GnomAD database, including 10,822 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 0.37 ( 10822 hom., cov: 32)

Consequence

MFAP3
ENST00000518497.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0300

Publications

4 publications found
Variant links:
Genes affected
MFAP3 (HGNC:7034): (microfibril associated protein 3) Predicted to be located in extracellular region. Predicted to be active in cytoplasm; nucleus; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 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
MFAP3ENST00000518497.6 linkn.249+8995T>C intron_variant Intron 1 of 3 4
MFAP3ENST00000519325.1 linkn.249+8995T>C intron_variant Intron 1 of 4 3
MFAP3ENST00000519612.5 linkn.249+8995T>C intron_variant Intron 1 of 3 4

Frequencies

GnomAD3 genomes
AF:
0.371
AC:
56309
AN:
151878
Hom.:
10811
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.399
Gnomad AMI
AF:
0.459
Gnomad AMR
AF:
0.336
Gnomad ASJ
AF:
0.402
Gnomad EAS
AF:
0.125
Gnomad SAS
AF:
0.306
Gnomad FIN
AF:
0.375
Gnomad MID
AF:
0.541
Gnomad NFE
AF:
0.379
Gnomad OTH
AF:
0.406
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.371
AC:
56338
AN:
151996
Hom.:
10822
Cov.:
32
AF XY:
0.367
AC XY:
27274
AN XY:
74284
show subpopulations
African (AFR)
AF:
0.399
AC:
16542
AN:
41444
American (AMR)
AF:
0.335
AC:
5115
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.402
AC:
1395
AN:
3470
East Asian (EAS)
AF:
0.125
AC:
645
AN:
5162
South Asian (SAS)
AF:
0.305
AC:
1470
AN:
4820
European-Finnish (FIN)
AF:
0.375
AC:
3962
AN:
10556
Middle Eastern (MID)
AF:
0.554
AC:
163
AN:
294
European-Non Finnish (NFE)
AF:
0.379
AC:
25776
AN:
67952
Other (OTH)
AF:
0.403
AC:
852
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1792
3584
5376
7168
8960
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
524
1048
1572
2096
2620
<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:
0.362
Hom.:
1640
Bravo
AF:
0.370
Asia WGS
AF:
0.238
AC:
827
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
5.2
DANN
Benign
0.83
PhyloP100
-0.030

Splicing

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

Publications

Other links and lift over

dbSNP: rs707184; hg19: chr5-153485826; API