NM_012425.4:c.731+47339C>T

Variant names:

• chr10-16647684-G-A
• rs7087965
• NM_012425.4:c.731+47339C>T

Variant summary

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

The NM_012425.4(RSU1):​c.731+47339C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,890 control chromosomes in the GnomAD database, including 8,660 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 0.33 (8660 hom., cov: 31)
• Consequence: RSU1 NM_012425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353
• Publications: 3 publications found

Genes affected

RSU1 (HGNC:10464): (Ras suppressor protein 1) This gene encodes a protein that is involved in the Ras signal transduction pathway, growth inhibition, and nerve-growth factor induced differentiation processes, as determined in mouse and human cell line studies. In mouse, the encoded protein was initially isolated based on its ability to inhibit v-Ras transformation. Multiple alternatively spliced transcript variants for this gene have been reported; one of these variants was found only in glioma tumors. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012425.4. 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
	RSU1	NM_012425.4	MANE Select	c.731+47339C>T		intron	N/A	NP_036557.1	Q15404-1
	RSU1	NM_152724.3		c.572+47339C>T		intron	N/A	NP_689937.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSU1	ENST00000345264.10	TSL:1 MANE Select	c.731+47339C>T		intron	N/A	ENSP00000339521.5	Q15404-1
	RSU1	ENST00000377921.7	TSL:1	c.731+47339C>T		intron	N/A	ENSP00000367154.3	Q15404-1
	RSU1	ENST00000602389.1	TSL:1	c.572+47339C>T		intron	N/A	ENSP00000473588.1	Q15404-2

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50124 AN: 151772 Hom.: 8645 Cov.: 31

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.330 AC: 50184 AN: 151890 Hom.: 8660 Cov.: 31 AF XY: 0.327 AC XY: 24297 AN XY: 74238

African (AFR) AF: 0.433 AC: 17904 AN: 41392

American (AMR) AF: 0.310 AC: 4725 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 911 AN: 3468

East Asian (EAS) AF: 0.314 AC: 1622 AN: 5162

South Asian (SAS) AF: 0.301 AC: 1442 AN: 4798

European-Finnish (FIN) AF: 0.252 AC: 2664 AN: 10554

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.293 AC: 19925 AN: 67958

Other (OTH) AF: 0.311 AC: 655 AN: 2108

Alfa AF: 0.309 Hom.: 17608

Bravo AF: 0.338

Asia WGS AF: 0.309 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.51
PhyloP100		-0.35
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: rs7087965; hg19: chr10-16689683;