chr5-179838216-C-T

Position:

• chr5-179838216-C-T

Variant summary

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

The ENST00000518219.5(MRNIP):​c.*2614G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0535 in 360,462 control chromosomes in the GnomAD database, including 626 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 0.061 (318 hom., cov: 33)
  • Exomes 𝑓: 0.048 (308 hom.)
• Consequence: MRNIP ENST00000518219.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MRNIP	NM_016175.4	c.538-331G>A		intron_variant		ENST00000292586.11	NP_057259.2
MRNIP	NM_001017987.3	c.373-331G>A		intron_variant			NP_001017987.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MRNIP	ENST00000292586.11	c.538-331G>A		intron_variant		1	NM_016175.4	ENSP00000292586	P2

Frequencies

GnomAD3 genomes AF: 0.0614 AC: 9348 AN: 152138 Hom.: 318 Cov.: 33

Gnomad AFR AF: 0.0843

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0626

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.0465

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0524

Gnomad OTH AF: 0.0644

GnomAD4 exome AF: 0.0477 AC: 9936 AN: 208206 Hom.: 308 Cov.: 0 AF XY: 0.0461 AC XY: 5005 AN XY: 108596

Gnomad4 AFR exome AF: 0.0852

Gnomad4 AMR exome AF: 0.0434

Gnomad4 ASJ exome AF: 0.0928

Gnomad4 EAS exome AF: 0.0000807

Gnomad4 SAS exome AF: 0.0239

Gnomad4 FIN exome AF: 0.0402

Gnomad4 NFE exome AF: 0.0524

Gnomad4 OTH exome AF: 0.0546

GnomAD4 genome AF: 0.0614 AC: 9349 AN: 152256 Hom.: 318 Cov.: 33 AF XY: 0.0599 AC XY: 4459 AN XY: 74448

Gnomad4 AFR AF: 0.0842

Gnomad4 AMR AF: 0.0626

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0282

Gnomad4 FIN AF: 0.0465

Gnomad4 NFE AF: 0.0524

Gnomad4 OTH AF: 0.0627

Alfa AF: 0.0555 Hom.: 172

Bravo AF: 0.0630

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.8
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs248244; hg19: chr5-179265216;