chr17-57335100-A-G

Variant names:

• chr17-57335100-A-G
• rs9890811
• NM_138962.4:c.313-66279A>G

Variant summary

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

The NM_138962.4(MSI2):​c.313-66279A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,158 control chromosomes in the GnomAD database, including 3,717 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 (3717 hom., cov: 32)
• Consequence: MSI2 NM_138962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 1 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSI2	NM_138962.4	MANE Select	c.313-66279A>G		intron	N/A	NP_620412.1
	MSI2	NM_001322250.2		c.247-66279A>G		intron	N/A	NP_001309179.1
	MSI2	NM_001322251.2		c.313-66279A>G		intron	N/A	NP_001309180.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSI2	ENST00000284073.7	TSL:1 MANE Select	c.313-66279A>G		intron	N/A	ENSP00000284073.2
	MSI2	ENST00000579180.2	TSL:1	c.-1+40311A>G		intron	N/A	ENSP00000462264.1
	MSI2	ENST00000675656.1		c.274-66279A>G		intron	N/A	ENSP00000501595.1

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23842 AN: 152042 Hom.: 3703 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.0556

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.0472

Gnomad FIN AF: 0.0585

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0363

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.157 AC: 23904 AN: 152158 Hom.: 3717 Cov.: 32 AF XY: 0.157 AC XY: 11684 AN XY: 74406

African (AFR) AF: 0.392 AC: 16250 AN: 41438

American (AMR) AF: 0.191 AC: 2918 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0556 AC: 193 AN: 3470

East Asian (EAS) AF: 0.181 AC: 936 AN: 5184

South Asian (SAS) AF: 0.0473 AC: 228 AN: 4822

European-Finnish (FIN) AF: 0.0585 AC: 621 AN: 10612

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0363 AC: 2468 AN: 68018

Other (OTH) AF: 0.126 AC: 266 AN: 2110

Alfa AF: 0.0653 Hom.: 1502

Bravo AF: 0.179

Asia WGS AF: 0.132 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.8
DANN	Benign	0.68
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs9890811; hg19: chr17-55412461;