Menu
GeneBe

rs17465637

Variant summary

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

The NM_198551.4(MIA3):c.3632-105A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 736,816 control chromosomes in the GnomAD database, including 165,801 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 ( 28044 hom., cov: 32)
Exomes 𝑓: 0.68 ( 137757 hom. )

Consequence

MIA3
NM_198551.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.629
Variant links:
Genes affected
MIA3 (HGNC:24008): (MIA SH3 domain ER export factor 3) Enables cargo receptor activity. Involved in several processes, including COPII-coated vesicle cargo loading; cell migration involved in sprouting angiogenesis; and regulation of leukocyte migration. Located in endoplasmic reticulum exit site and endoplasmic reticulum membrane. Is integral component of 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=-0.94).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MIA3NM_198551.4 linkuse as main transcriptc.3632-105A>C intron_variant ENST00000344922.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MIA3ENST00000344922.10 linkuse as main transcriptc.3632-105A>C intron_variant 5 NM_198551.4 P1Q5JRA6-1

Frequencies

GnomAD3 genomes
AF:
0.572
AC:
86881
AN:
151940
Hom.:
28034
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.258
Gnomad AMI
AF:
0.781
Gnomad AMR
AF:
0.559
Gnomad ASJ
AF:
0.715
Gnomad EAS
AF:
0.595
Gnomad SAS
AF:
0.603
Gnomad FIN
AF:
0.750
Gnomad MID
AF:
0.646
Gnomad NFE
AF:
0.723
Gnomad OTH
AF:
0.586
GnomAD3 exomes
AF:
0.643
AC:
99728
AN:
155216
Hom.:
33331
AF XY:
0.651
AC XY:
53444
AN XY:
82086
show subpopulations
Gnomad AFR exome
AF:
0.249
Gnomad AMR exome
AF:
0.496
Gnomad ASJ exome
AF:
0.717
Gnomad EAS exome
AF:
0.596
Gnomad SAS exome
AF:
0.624
Gnomad FIN exome
AF:
0.748
Gnomad NFE exome
AF:
0.725
Gnomad OTH exome
AF:
0.658
GnomAD4 exome
AF:
0.679
AC:
396789
AN:
584758
Hom.:
137757
Cov.:
7
AF XY:
0.681
AC XY:
214251
AN XY:
314462
show subpopulations
Gnomad4 AFR exome
AF:
0.262
Gnomad4 AMR exome
AF:
0.498
Gnomad4 ASJ exome
AF:
0.719
Gnomad4 EAS exome
AF:
0.562
Gnomad4 SAS exome
AF:
0.630
Gnomad4 FIN exome
AF:
0.747
Gnomad4 NFE exome
AF:
0.726
Gnomad4 OTH exome
AF:
0.660
GnomAD4 genome
AF:
0.571
AC:
86897
AN:
152058
Hom.:
28044
Cov.:
32
AF XY:
0.573
AC XY:
42603
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.257
Gnomad4 AMR
AF:
0.559
Gnomad4 ASJ
AF:
0.715
Gnomad4 EAS
AF:
0.596
Gnomad4 SAS
AF:
0.604
Gnomad4 FIN
AF:
0.750
Gnomad4 NFE
AF:
0.723
Gnomad4 OTH
AF:
0.587
Alfa
AF:
0.695
Hom.:
73119
Bravo
AF:
0.541
Asia WGS
AF:
0.545
AC:
1897
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
Cadd
Benign
0.059
Dann
Benign
0.56

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

LitVar

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

Other links and lift over

dbSNP: rs17465637; hg19: chr1-222823529; API