17-57493596-G-A

Position:

• chr17-57493596-G-A

Variant summary

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

The NM_138962.4(MSI2):​c.406-36080G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.906 in 149,638 control chromosomes in the GnomAD database, including 61,449 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 0.91 (61449 hom., cov: 25)
• Consequence: MSI2 NM_138962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714

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 (AFR) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSI2	NM_138962.4	c.406-36080G>A		intron_variant		ENST00000284073.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSI2	ENST00000284073.7	c.406-36080G>A		intron_variant		1	NM_138962.4	P1

Frequencies

GnomAD3 genomes AF: 0.906 AC: 135399 AN: 149520 Hom.: 61398 Cov.: 25

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.898

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.916

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.906 AC: 135504 AN: 149638 Hom.: 61449 Cov.: 25 AF XY: 0.906 AC XY: 65962 AN XY: 72780

Gnomad4 AFR AF: 0.961

Gnomad4 AMR AF: 0.900

Gnomad4 ASJ AF: 0.898

Gnomad4 EAS AF: 0.839

Gnomad4 SAS AF: 0.887

Gnomad4 FIN AF: 0.916

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.913

Alfa AF: 0.887 Hom.: 41898

Bravo AF: 0.906

Asia WGS AF: 0.867 AC: 3014 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	0.39
DANN	Benign	0.43

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: rs933534; hg19: chr17-55570957;