17-57670055-G-A

Variant names:

• chr17-57670055-G-A
• rs11079321
• NM_138962.4:c.791-4917G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138962.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSI2	NM_138962.4	MANE Select	c.791-4917G>A		intron	N/A	NP_620412.1	Q96DH6-1
	MSI2	NM_001322250.2		c.725-4863G>A		intron	N/A	NP_001309179.1	B4DHE8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSI2	ENST00000284073.7	TSL:1 MANE Select	c.791-4917G>A		intron	N/A	ENSP00000284073.2	Q96DH6-1
	MSI2	ENST00000902711.1		c.875-4917G>A		intron	N/A	ENSP00000572770.1
	MSI2	ENST00000902712.1		c.779-4863G>A		intron	N/A	ENSP00000572771.1

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

African (AFR) AF: 0.271 AC: 11249 AN: 41478

American (AMR) AF: 0.377 AC: 5769 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 944 AN: 3466

East Asian (EAS) AF: 0.422 AC: 2179 AN: 5166

South Asian (SAS) AF: 0.327 AC: 1574 AN: 4818

European-Finnish (FIN) AF: 0.295 AC: 3126 AN: 10590

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17337 AN: 67988

Other (OTH) AF: 0.278 AC: 585 AN: 2108

Alfa AF: 0.274 Hom.: 4206

Bravo AF: 0.291

Asia WGS AF: 0.377 AC: 1310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.12
DANN	Benign	0.42
PhyloP100		-1.0
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: rs11079321; hg19: chr17-55747416;