5-179846265-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MRNIP	NM_016175.4	c.215+1713G>A		intron_variant		ENST00000292586.11
MRNIP	NM_001017987.3	c.127-4201G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MRNIP	ENST00000292586.11	c.215+1713G>A		intron_variant		1	NM_016175.4	P2

Frequencies

GnomAD3 genomes AF: 0.0665 AC: 10033 AN: 150940 Hom.: 368 Cov.: 31

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: 6 AN: 28 Hom.: 1 AF XY: 0.208 AC XY: 5 AN XY: 24

Gnomad4 ASJ exome AF: 0.500

Gnomad4 NFE exome AF: 0.227

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0664 AC: 10030 AN: 151014 Hom.: 368 Cov.: 31 AF XY: 0.0640 AC XY: 4721 AN XY: 73726

Gnomad4 AFR AF: 0.0763

Gnomad4 AMR AF: 0.0705

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.000969

Gnomad4 SAS AF: 0.0341

Gnomad4 FIN AF: 0.0487

Gnomad4 NFE AF: 0.0654

Gnomad4 OTH AF: 0.0730

Alfa AF: 0.0563 Hom.: 177

Bravo AF: 0.0677

Asia WGS AF: 0.0190 AC: 67 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	2.0
Dann	Benign	0.70

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

LitVar

Other links and lift over

dbSNP: rs155793; hg19: chr5-179273265;