rs7908112

Variant names:

• chr10-16789495-A-G
• rs7908112
• NM_012425.4:c.110-7411T>C

Variant summary

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

The NM_012425.4(RSU1):​c.110-7411T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 152,148 control chromosomes in the GnomAD database, including 17,729 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 0.44 (17729 hom., cov: 33)
• Consequence: RSU1 NM_012425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 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.110-7411T>C		intron	N/A	NP_036557.1
	RSU1	NM_152724.3		c.-50-7411T>C		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.110-7411T>C		intron	N/A	ENSP00000339521.5
	RSU1	ENST00000377921.7	TSL:1	c.110-7411T>C		intron	N/A	ENSP00000367154.3
	RSU1	ENST00000602389.1	TSL:1	c.-50-7411T>C		intron	N/A	ENSP00000473588.1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66171 AN: 152030 Hom.: 17674 Cov.: 33

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.436 AC: 66295 AN: 152148 Hom.: 17729 Cov.: 33 AF XY: 0.433 AC XY: 32179 AN XY: 74384

African (AFR) AF: 0.768 AC: 31879 AN: 41490

American (AMR) AF: 0.359 AC: 5483 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1049 AN: 3468

East Asian (EAS) AF: 0.443 AC: 2291 AN: 5174

South Asian (SAS) AF: 0.321 AC: 1550 AN: 4824

European-Finnish (FIN) AF: 0.297 AC: 3147 AN: 10588

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19668 AN: 67998

Other (OTH) AF: 0.409 AC: 864 AN: 2112

Alfa AF: 0.383 Hom.: 1789

Bravo AF: 0.456

Asia WGS AF: 0.415 AC: 1440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.38
DANN	Benign	0.65
PhyloP100		-0.81
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: rs7908112; hg19: chr10-16831494;