chr5-179846820-G-A

Position:

• chr5-179846820-G-A

Variant summary

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

The NM_016175.4(MRNIP):​c.215+1158C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,920 control chromosomes in the GnomAD database, including 14,560 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 0.42 (14560 hom., cov: 31)
• Consequence: MRNIP NM_016175.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.741

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MRNIP	NM_016175.4	c.215+1158C>T		intron_variant		ENST00000292586.11	NP_057259.2
MRNIP	NM_001017987.3	c.127-4756C>T		intron_variant			NP_001017987.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MRNIP	ENST00000292586.11	c.215+1158C>T		intron_variant		1	NM_016175.4	ENSP00000292586	P2

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63167 AN: 151802 Hom.: 14543 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.416 AC: 63195 AN: 151920 Hom.: 14560 Cov.: 31 AF XY: 0.429 AC XY: 31867 AN XY: 74218

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.413

Alfa AF: 0.439 Hom.: 31855

Bravo AF: 0.409

Asia WGS AF: 0.643 AC: 2235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.73

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: rs748197; hg19: chr5-179273820;