5-179846265-C-T

Variant names:

• chr5-179846265-C-T
• rs155793
• NM_016175.4:c.215+1713G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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]

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

ACMG classification

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRNIP	NM_016175.4	c.215+1713G>A		intron_variant	Intron 3 of 6	ENST00000292586.11	NP_057259.2
MRNIP	NM_001017987.3	c.127-4201G>A		intron_variant	Intron 2 of 4		NP_001017987.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRNIP	ENST00000292586.11	c.215+1713G>A		intron_variant	Intron 3 of 6	1	NM_016175.4	ENSP00000292586.6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.227 AC: 5 AN: 22

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

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: 5 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: 37 AN: 286

European-Non Finnish (NFE) AF: 0.0654 AC: 4433 AN: 67812

Other (OTH) AF: 0.0730 AC: 152 AN: 2082

Alfa AF: 0.0579 Hom.: 206

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
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs155793; hg19: chr5-179273265;