NM_012425.4:c.598+9728G>A

Variant names:

• chr10-16742811-C-T
• rs7911748
• NM_012425.4:c.598+9728G>A

Variant summary

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

The NM_012425.4(RSU1):​c.598+9728G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,060 control chromosomes in the GnomAD database, including 4,043 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 0.22 (4043 hom., cov: 32)
• Consequence: RSU1 NM_012425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 2 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]

ENSG00000225213 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSU1	NM_012425.4	MANE Select	c.598+9728G>A		intron	N/A	NP_036557.1
	RSU1	NM_152724.3		c.439+9728G>A		intron	N/A	NP_689937.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSU1	ENST00000345264.10	TSL:1 MANE Select	c.598+9728G>A		intron	N/A	ENSP00000339521.5
	RSU1	ENST00000377921.7	TSL:1	c.598+9728G>A		intron	N/A	ENSP00000367154.3
	RSU1	ENST00000602389.1	TSL:1	c.439+9728G>A		intron	N/A	ENSP00000473588.1

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33585 AN: 151942 Hom.: 4037 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.221 AC: 33636 AN: 152060 Hom.: 4043 Cov.: 32 AF XY: 0.222 AC XY: 16466 AN XY: 74332

African (AFR) AF: 0.304 AC: 12613 AN: 41448

American (AMR) AF: 0.217 AC: 3319 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 751 AN: 3466

East Asian (EAS) AF: 0.210 AC: 1086 AN: 5162

South Asian (SAS) AF: 0.0969 AC: 468 AN: 4830

European-Finnish (FIN) AF: 0.210 AC: 2223 AN: 10564

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12377 AN: 68004

Other (OTH) AF: 0.220 AC: 466 AN: 2114

Alfa AF: 0.195 Hom.: 3840

Bravo AF: 0.227

Asia WGS AF: 0.154 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.67
PhyloP100		-0.19
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: rs7911748; hg19: chr10-16784810;