chr17-17184566-T-G

Variant names:

• chr17-17184566-T-G
• rs4985741
• NM_001364716.4:c.7207-257T>G

Variant summary

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

The NM_001364716.4(MPRIP):​c.7207-257T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 152,164 control chromosomes in the GnomAD database, including 25,179 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 0.53 (25179 hom., cov: 33)
• Consequence: MPRIP NM_001364716.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 6 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]

ENSG00000263624 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPRIP	NM_001364716.4	c.7207-257T>G		intron_variant	Intron 23 of 23	ENST00000651222.2	NP_001351645.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPRIP	ENST00000651222.2	c.7207-257T>G		intron_variant	Intron 23 of 23		NM_001364716.4	ENSP00000498253.1

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80118 AN: 152046 Hom.: 25187 Cov.: 33

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.526 AC: 80106 AN: 152164 Hom.: 25179 Cov.: 33 AF XY: 0.534 AC XY: 39767 AN XY: 74410

African (AFR) AF: 0.164 AC: 6820 AN: 41532

American (AMR) AF: 0.580 AC: 8862 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2218 AN: 3468

East Asian (EAS) AF: 0.684 AC: 3546 AN: 5182

South Asian (SAS) AF: 0.615 AC: 2962 AN: 4814

European-Finnish (FIN) AF: 0.783 AC: 8291 AN: 10594

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45383 AN: 67968

Other (OTH) AF: 0.540 AC: 1138 AN: 2108

Alfa AF: 0.609 Hom.: 15779

Bravo AF: 0.492

Asia WGS AF: 0.609 AC: 2114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	11
DANN	Benign	0.78
PhyloP100		0.23
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: rs4985741; hg19: chr17-17087880;