rs9892791

chr17-57417734-C-Achr17-57417734-C-Gchr17-57417734-C-T

Variant summary

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

The NM_138962.4(MSI2):c.405+16263C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,006 control chromosomes in the GnomAD database, including 36,610 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 0.69 (36610 hom., cov: 31)
• Consequence: MSI2 NM_138962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSI2	NM_138962.4	c.405+16263C>A		intron_variant		ENST00000284073.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSI2	ENST00000284073.7	c.405+16263C>A		intron_variant		1	NM_138962.4	P1

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105037 AN: 151888 Hom.: 36582 Cov.: 31

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.692 AC: 105120 AN: 152006 Hom.: 36610 Cov.: 31 AF XY: 0.696 AC XY: 51699 AN XY: 74288

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.743

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.790

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.712

Alfa AF: 0.694 Hom.: 46913

Bravo AF: 0.701

Asia WGS AF: 0.837 AC: 2911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.4
Dann	Benign	0.59
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs9892791; hg19: chr17-55495095;