5-179840947-CCT-ACG

Variant names:

• chr5-179840947-CCT-ACG
• NM_016175.4:c.460_462delAGGinsCGT
• MRNIP p.155

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP7

The NM_016175.4(MRNIP):​c.460_462delAGGinsCGT​(p.155) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 30)
• Consequence: MRNIP NM_016175.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.607
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP7: Synonymous conserved (PhyloP=0.607 with no splicing effect.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRNIP	NM_016175.4	MANE Select	c.460_462delAGGinsCGT	p.155	synonymous	N/A	NP_057259.2	Q6NTE8-1
	MRNIP	NM_001017987.3		c.295_297delAGGinsCGT	p.100	synonymous	N/A	NP_001017987.1	Q6NTE8-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MRNIP	ENST00000292586.11	TSL:1 MANE Select	c.460_462delAGGinsCGT	p.155	synonymous	N/A	ENSP00000292586.6	Q6NTE8-1
	MRNIP	ENST00000523084.5	TSL:1	c.58_60delAGGinsCGT	p.21	synonymous	N/A	ENSP00000429107.1	E5RJC6
	MRNIP	ENST00000518219.5	TSL:1	c.460_462delAGGinsCGT	p.155	synonymous	N/A	ENSP00000428460.1	E5RI52

Frequencies

GnomAD3 genomes Cov.: 30

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.61

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr5-179267947;