rs11079321

Positions:

• chr17-57670055-G-A
• chr17-57670055-G-C
• chr17-57670055-G-T

Variant summary

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

The NM_138962.4(MSI2):​c.791-4917G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,102 control chromosomes in the GnomAD database, including 6,385 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 0.28 (6385 hom., cov: 33)
• Consequence: MSI2 NM_138962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

MSI2 (HGNC:18585): (musashi RNA binding protein 2) This gene encodes an RNA-binding protein that is a member of the Musashi protein family. The encoded protein is transcriptional regulator that targets genes involved in development and cell cycle regulation. Mutations in this gene are associated with poor prognosis in certain types of cancers. This gene has also been shown to be rearranged in certain cancer cells. [provided by RefSeq, Apr 2016]

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 = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSI2	NM_138962.4	c.791-4917G>A		intron_variant		ENST00000284073.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSI2	ENST00000284073.7	c.791-4917G>A		intron_variant		1	NM_138962.4	P1

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43108 AN: 151982 Hom.: 6375 Cov.: 33

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.284 AC: 43140 AN: 152102 Hom.: 6385 Cov.: 33 AF XY: 0.288 AC XY: 21437 AN XY: 74366

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.278

Alfa AF: 0.272 Hom.: 2884

Bravo AF: 0.291

Asia WGS AF: 0.377 AC: 1310 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	0.12
DANN	Benign	0.42

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: rs11079321; hg19: chr17-55747416;