NM_001364716.4:c.3277G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBS1BS2

The NM_001364716.4(MPRIP):​c.3277G>A​(p.Val1093Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00124 in 1,304,052 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 6/6 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0061 ( 15 hom., cov: 33)
Exomes 𝑓: 0.00059 ( 2 hom. )

Consequence

MPRIP
NM_001364716.4 missense

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.502

Publications

10 publications found
Variant links:
Genes affected
MPRIP (HGNC:30321): (myosin phosphatase Rho interacting protein) Enables cadherin binding activity. Predicted to be involved in actin filament organization. Located in actin cytoskeleton and cytosol. [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 -10 ACMG points.

BP4
Computational evidence support a benign effect (REVEL=0.063).
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00614 (935/152384) while in subpopulation AFR AF = 0.0213 (887/41592). AF 95% confidence interval is 0.0202. There are 15 homozygotes in GnomAd4. There are 461 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 15 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MPRIPNM_001364716.4 linkc.3277G>A p.Val1093Met missense_variant Exon 16 of 24 ENST00000651222.2 NP_001351645.2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MPRIPENST00000651222.2 linkc.3277G>A p.Val1093Met missense_variant Exon 16 of 24 NM_001364716.4 ENSP00000498253.1 A0A494BZV2

Frequencies

GnomAD3 genomes
AF:
0.00611
AC:
931
AN:
152266
Hom.:
15
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0213
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00229
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000588
Gnomad OTH
AF:
0.00382
GnomAD2 exomes
AF:
0.00122
AC:
179
AN:
146860
AF XY:
0.000935
show subpopulations
Gnomad AFR exome
AF:
0.0215
Gnomad AMR exome
AF:
0.00102
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000111
Gnomad OTH exome
AF:
0.000235
GnomAD4 exome
AF:
0.000587
AC:
676
AN:
1151668
Hom.:
2
Cov.:
29
AF XY:
0.000510
AC XY:
288
AN XY:
564688
show subpopulations
African (AFR)
AF:
0.0228
AC:
556
AN:
24412
American (AMR)
AF:
0.000920
AC:
26
AN:
28258
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
15934
East Asian (EAS)
AF:
0.00
AC:
0
AN:
12844
South Asian (SAS)
AF:
0.000171
AC:
13
AN:
76160
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
27178
Middle Eastern (MID)
AF:
0.000909
AC:
4
AN:
4402
European-Non Finnish (NFE)
AF:
0.0000239
AC:
22
AN:
920866
Other (OTH)
AF:
0.00132
AC:
55
AN:
41614
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.491
Heterozygous variant carriers
0
44
88
133
177
221
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
28
56
84
112
140
<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:
0.00614
AC:
935
AN:
152384
Hom.:
15
Cov.:
33
AF XY:
0.00619
AC XY:
461
AN XY:
74520
show subpopulations
African (AFR)
AF:
0.0213
AC:
887
AN:
41592
American (AMR)
AF:
0.00229
AC:
35
AN:
15310
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3472
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5186
South Asian (SAS)
AF:
0.000207
AC:
1
AN:
4834
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10628
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
0.0000588
AC:
4
AN:
68042
Other (OTH)
AF:
0.00378
AC:
8
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
46
92
138
184
230
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
20
40
60
80
100
<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:
0.00385
Hom.:
30
Bravo
AF:
0.00684

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.58
CADD
Benign
5.7
DANN
Benign
0.80
PhyloP100
0.50
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
Mutation Taster
=99/1
polymorphism

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

Other links and lift over

dbSNP: rs61744862; hg19: chr17-17068182; API