Genetic Variant MRNIP:c.215+1713G>A (chr5-179846265-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.215+1713G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0664 in 151,042 control chromosomes in the GnomAD database, including 369 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 0.066 ( 368 hom., cov: 31)

Exomes 𝑓: 0.21 ( 1 hom. )

Consequence

MRNIP
NM_016175.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.145

Publications

5 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:

RN7SKP150 (HGNC:45874): (RN7SK pseudogene 150)

RN7SKP150 links:

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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 (AFR) allele frequency at 95% confidence interval = 0.0741 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016175.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRNIP	NM_016175.4	MANE Select	c.215+1713G>A		intron	N/A	NP_057259.2
	MRNIP	NM_001017987.3		c.127-4201G>A		intron	N/A	NP_001017987.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MRNIP	ENST00000292586.11	TSL:1 MANE Select	c.215+1713G>A	intron	N/A	ENSP00000292586.6
MRNIP	ENST00000523084.5	TSL:1	c.-187-2038G>A	intron	N/A	ENSP00000429107.1
MRNIP	ENST00000518219.5	TSL:1	c.215+1713G>A	intron	N/A	ENSP00000428460.1

Frequencies

GnomAD3 genomes

AF:

0.0665

AC:

10033

AN:

150940

Hom.:

368

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0764

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.0705

Gnomad ASJ

AF:

0.113

Gnomad EAS

AF:

0.000966

Gnomad SAS

AF:

0.0343

Gnomad FIN

AF:

0.0487

Gnomad MID

AF:

0.125

Gnomad NFE

AF:

0.0654

Gnomad OTH

AF:

0.0747

GnomAD4 exome

AF:

0.214

AC:

AN:

Hom.:

AF XY:

0.208

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.227

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.450

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0664

AC:

10030

AN:

151014

Hom.:

368

Cov.:

AF XY:

0.0640

AC XY:

4721

AN XY:

73726

show subpopulations

African (AFR)

AF:

0.0763

AC:

3145

AN:

41210

American (AMR)

AF:

0.0705

AC:

1065

AN:

15102

Ashkenazi Jewish (ASJ)

AF:

0.113

AC:

390

AN:

3454

East Asian (EAS)

AF:

0.000969

AC:

AN:

5162

South Asian (SAS)

AF:

0.0341

AC:

163

AN:

4784

European-Finnish (FIN)

AF:

0.0487

AC:

497

AN:

10210

Middle Eastern (MID)

AF:

0.129

AC:

AN:

286

European-Non Finnish (NFE)

AF:

0.0654

AC:

4433

AN:

67812

Other (OTH)

AF:

0.0730

AC:

152

AN:

2082

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

479

959

1438

1918

2397

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

224

336

448

560

<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:

0.0579

Hom.:

206

Bravo

AF:

0.0677

Asia WGS

AF:

0.0190

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.0

(source)

DANN

Benign

0.70

PhyloP100

0.14

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over