dbSNP rs2303677: MRNIP:c.449+128G>A (chr5-179841779-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_016175.4(MRNIP):c.449+128G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 990,722 control chromosomes in the GnomAD database, including 33,449 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 0.22 ( 4677 hom., cov: 32)

Exomes 𝑓: 0.24 ( 28772 hom. )

Consequence

MRNIP
NM_016175.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0220

Publications

11 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 = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRNIP	NM_016175.4 link	c.449+128G>A		intron_variant	Intron 5 of 6	ENST00000292586.11	NP_057259.2
MRNIP	NM_001017987.3 link	c.284+128G>A		intron_variant	Intron 3 of 4		NP_001017987.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRNIP	ENST00000292586.11 link	c.449+128G>A		intron_variant	Intron 5 of 6	1	NM_016175.4	ENSP00000292586.6

Frequencies

GnomAD3 genomes

AF:

0.220

AC:

33367

AN:

152006

Hom.:

4671

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0930

Gnomad AMI

AF:

0.199

Gnomad AMR

AF:

0.386

Gnomad ASJ

AF:

0.259

Gnomad EAS

AF:

0.516

Gnomad SAS

AF:

0.383

Gnomad FIN

AF:

0.293

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.212

Gnomad OTH

AF:

0.220

GnomAD4 exome

AF:

0.244

AC:

204936

AN:

838598

Hom.:

28772

Cov.:

AF XY:

0.249

AC XY:

106978

AN XY:

429656

show subpopulations

African (AFR)

AF:

0.0880

AC:

1768

AN:

20096

American (AMR)

AF:

0.488

AC:

13163

AN:

26968

Ashkenazi Jewish (ASJ)

AF:

0.251

AC:

4188

AN:

16656

East Asian (EAS)

AF:

0.495

AC:

18059

AN:

36468

South Asian (SAS)

AF:

0.380

AC:

22455

AN:

59094

European-Finnish (FIN)

AF:

0.284

AC:

12791

AN:

45070

Middle Eastern (MID)

AF:

0.214

AC:

578

AN:

2706

European-Non Finnish (NFE)

AF:

0.207

AC:

122548

AN:

592812

Other (OTH)

AF:

0.242

AC:

9386

AN:

38728

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

7444

14888

22332

29776

37220

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3392

6784

10176

13568

16960

<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:

0.219

AC:

33382

AN:

152124

Hom.:

4677

Cov.:

AF XY:

0.232

AC XY:

17217

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.0929

AC:

3861

AN:

41544

American (AMR)

AF:

0.386

AC:

5896

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.259

AC:

898

AN:

3472

East Asian (EAS)

AF:

0.516

AC:

2645

AN:

5124

South Asian (SAS)

AF:

0.381

AC:

1832

AN:

4804

European-Finnish (FIN)

AF:

0.293

AC:

3101

AN:

10588

Middle Eastern (MID)

AF:

0.180

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.212

AC:

14437

AN:

67994

Other (OTH)

AF:

0.227

AC:

478

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1265

2530

3794

5059

6324

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

358

716

1074

1432

1790

<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:

0.214

Hom.:

3478

Bravo

AF:

0.219

Asia WGS

AF:

0.423

AC:

1470

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

5.0

(source)

DANN

Benign

0.75

PhyloP100

0.022

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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