rs6502557

Variant names:

• chr17-17057664-G-A
• rs6502557
• NM_001364716.4:c.123+14693G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-17057664-G-A
• chr17-17057664-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001364716.4(MPRIP):​c.123+14693G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 717,724 control chromosomes in the GnomAD database, including 8,947 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 0.16 (2055 hom., cov: 32)
  • Exomes 𝑓: 0.15 (6892 hom.)
• Consequence: MPRIP NM_001364716.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71
• Publications: 20 publications found

Genes affected

MPRIP (HGNC:30321): (myosin phosphatase Rho interacting protein) Enables cadherin binding activity. Predicted to be involved in actin filament organization. Located in actin cytoskeleton and cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0033490062).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPRIP	NM_001364716.4	c.123+14693G>A		intron_variant	Intron 1 of 23	ENST00000651222.2	NP_001351645.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPRIP	ENST00000651222.2	c.123+14693G>A		intron_variant	Intron 1 of 23		NM_001364716.4	ENSP00000498253.1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24402 AN: 151848 Hom.: 2052 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.188

GnomAD2 exomes AF: 0.146 AC: 22136 AN: 151582 AF XY: 0.147

Gnomad AFR exome AF: 0.193

Gnomad AMR exome AF: 0.119

Gnomad ASJ exome AF: 0.224

Gnomad EAS exome AF: 0.127

Gnomad FIN exome AF: 0.141

Gnomad NFE exome AF: 0.156

Gnomad OTH exome AF: 0.171

GnomAD4 exome AF: 0.151 AC: 85622 AN: 565758 Hom.: 6892 Cov.: 0 AF XY: 0.151 AC XY: 45964 AN XY: 305214

African (AFR) AF: 0.184 AC: 2904 AN: 15808

American (AMR) AF: 0.125 AC: 4334 AN: 34720

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 4547 AN: 20030

East Asian (EAS) AF: 0.125 AC: 4006 AN: 32106

South Asian (SAS) AF: 0.116 AC: 7266 AN: 62772

European-Finnish (FIN) AF: 0.141 AC: 6780 AN: 48184

Middle Eastern (MID) AF: 0.211 AC: 860 AN: 4082

European-Non Finnish (NFE) AF: 0.156 AC: 49631 AN: 317168

Other (OTH) AF: 0.171 AC: 5294 AN: 30888

GnomAD4 genome AF: 0.161 AC: 24413 AN: 151966 Hom.: 2055 Cov.: 32 AF XY: 0.161 AC XY: 11939 AN XY: 74270

African (AFR) AF: 0.180 AC: 7446 AN: 41410

American (AMR) AF: 0.160 AC: 2439 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 768 AN: 3470

East Asian (EAS) AF: 0.121 AC: 623 AN: 5164

South Asian (SAS) AF: 0.107 AC: 517 AN: 4816

European-Finnish (FIN) AF: 0.152 AC: 1600 AN: 10556

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10369 AN: 67972

Other (OTH) AF: 0.189 AC: 397 AN: 2096

Alfa AF: 0.160 Hom.: 5881

Bravo AF: 0.168

TwinsUK AF: 0.157 AC: 583

ALSPAC AF: 0.144 AC: 554

ExAC AF: 0.134 AC: 2906

Asia WGS AF: 0.117 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.060
BayesDel_addAF	Benign	-0.79	T
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.045
DANN	Benign	0.51
DEOGEN2	Benign	0.029	T
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.00022	N
LIST_S2	Benign	0.28	T
MetaRNN	Benign	0.0033	T
MetaSVM	Benign	-1.0	T
PhyloP100		-2.7
PROVEAN	Benign	-0.75	N
REVEL	Benign	0.014
Sift	Pathogenic	0.0	D
Vest4		0.015
ClinPred		0.0044	T
GERP RS		-1.5
Mutation Taster		=89/11	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: rs6502557; hg19: chr17-16960978; COSMIC: COSV59044965;