dbSNP rs248247: MRNIP:c.*47C>T (chr5-179840783-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000518219.5(MRNIP):c.*47C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 999,016 control chromosomes in the GnomAD database, including 63,339 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 0.32 ( 8241 hom., cov: 33)

Exomes 𝑓: 0.35 ( 55098 hom. )

Consequence

MRNIP
ENST00000518219.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.38

Publications

19 publications found

Variant links:

Genes affected

MRNIP (HGNC:30817): (MRN complex interacting protein) Enables chromatin binding activity. Involved in several processes, including mitotic G2 DNA damage checkpoint signaling; regulation of double-strand break repair; and response to ionizing radiation. Located in nucleoplasm. Colocalizes with Mre11 complex. [provided by Alliance of Genome Resources, Apr 2022]

MRNIP 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRNIP	NM_016175.4 link	c.537+89C>T		intron_variant	Intron 6 of 6	ENST00000292586.11	NP_057259.2
MRNIP	NM_001017987.3 link	c.372+89C>T		intron_variant	Intron 4 of 4		NP_001017987.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRNIP	ENST00000292586.11 link	c.537+89C>T		intron_variant	Intron 6 of 6	1	NM_016175.4	ENSP00000292586.6		Q6NTE8-1

Frequencies

GnomAD3 genomes

AF:

0.317

AC:

48011

AN:

151676

Hom.:

8235

Cov.:

show subpopulations

Gnomad AFR

AF:

0.200

Gnomad AMI

AF:

0.234

Gnomad AMR

AF:

0.258

Gnomad ASJ

AF:

0.342

Gnomad EAS

AF:

0.479

Gnomad SAS

AF:

0.401

Gnomad FIN

AF:

0.463

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.361

Gnomad OTH

AF:

0.289

GnomAD2 exomes

AF:

0.354

AC:

52209

AN:

147398

AF XY:

0.360

show subpopulations

Gnomad AFR exome

AF:

0.193

Gnomad AMR exome

AF:

0.259

Gnomad ASJ exome

AF:

0.342

Gnomad EAS exome

AF:

0.481

Gnomad FIN exome

AF:

0.464

Gnomad NFE exome

AF:

0.352

Gnomad OTH exome

AF:

0.331

GnomAD4 exome

AF:

0.355

AC:

300749

AN:

847222

Hom.:

55098

Cov.:

AF XY:

0.358

AC XY:

155884

AN XY:

435756

show subpopulations

African (AFR)

AF:

0.192

AC:

4054

AN:

21142

American (AMR)

AF:

0.256

AC:

8774

AN:

34256

Ashkenazi Jewish (ASJ)

AF:

0.331

AC:

7005

AN:

21132

East Asian (EAS)

AF:

0.437

AC:

14450

AN:

33086

South Asian (SAS)

AF:

0.396

AC:

26741

AN:

67486

European-Finnish (FIN)

AF:

0.459

AC:

21780

AN:

47496

Middle Eastern (MID)

AF:

0.267

AC:

1214

AN:

4548

European-Non Finnish (NFE)

AF:

0.352

AC:

203459

AN:

578324

Other (OTH)

AF:

0.334

AC:

13272

AN:

39752

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

10158

20316

30474

40632

50790

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4684

9368

14052

18736

23420

<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:

0.316

AC:

48030

AN:

151794

Hom.:

8241

Cov.:

AF XY:

0.325

AC XY:

24076

AN XY:

74178

show subpopulations

African (AFR)

AF:

0.200

AC:

8255

AN:

41368

American (AMR)

AF:

0.257

AC:

3903

AN:

15172

Ashkenazi Jewish (ASJ)

AF:

0.342

AC:

1186

AN:

3470

East Asian (EAS)

AF:

0.479

AC:

2472

AN:

5162

South Asian (SAS)

AF:

0.400

AC:

1926

AN:

4820

European-Finnish (FIN)

AF:

0.463

AC:

4899

AN:

10586

Middle Eastern (MID)

AF:

0.241

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.361

AC:

24487

AN:

67914

Other (OTH)

AF:

0.295

AC:

619

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1673

3346

5019

6692

8365

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

502

1004

1506

2008

2510

<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:

0.332

Hom.:

16455

Bravo

AF:

0.290

Asia WGS

AF:

0.410

AC:

1425

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.22

(source)

DANN

Benign

0.70

PhyloP100

-1.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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