Genetic Variant ENST00000518219.5: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

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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