ENST00000519325.1:n.402+13960A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000519325.1(MFAP3):​n.402+13960A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,236 control chromosomes in the GnomAD database, including 26,230 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 0.57 ( 26230 hom., cov: 34)

Consequence

MFAP3
ENST00000519325.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.11
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 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
MFAP3ENST00000519325.1 linkn.402+13960A>G intron_variant Intron 3 of 4 3

Frequencies

GnomAD3 genomes
AF:
0.569
AC:
86581
AN:
152118
Hom.:
26202
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.700
Gnomad AMI
AF:
0.739
Gnomad AMR
AF:
0.395
Gnomad ASJ
AF:
0.482
Gnomad EAS
AF:
0.0371
Gnomad SAS
AF:
0.516
Gnomad FIN
AF:
0.594
Gnomad MID
AF:
0.665
Gnomad NFE
AF:
0.572
Gnomad OTH
AF:
0.550
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.569
AC:
86661
AN:
152236
Hom.:
26230
Cov.:
34
AF XY:
0.563
AC XY:
41910
AN XY:
74442
show subpopulations
Gnomad4 AFR
AF:
0.700
Gnomad4 AMR
AF:
0.394
Gnomad4 ASJ
AF:
0.482
Gnomad4 EAS
AF:
0.0372
Gnomad4 SAS
AF:
0.515
Gnomad4 FIN
AF:
0.594
Gnomad4 NFE
AF:
0.572
Gnomad4 OTH
AF:
0.548
Alfa
AF:
0.531
Hom.:
3776
Bravo
AF:
0.556
Asia WGS
AF:
0.338
AC:
1178
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.0090
DANN
Benign
0.21

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7708584; hg19: chr5-153543466; API