rs7911748

chr10-16742811-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSU1	NM_012425.4	c.598+9728G>A		intron_variant		ENST00000345264.10
RSU1	NM_152724.3	c.439+9728G>A		intron_variant
RSU1	XM_047425617.1	c.598+9728G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSU1	ENST00000345264.10	c.598+9728G>A		intron_variant		1	NM_012425.4	P1
	ENST00000421480.2	n.208+5359G>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.0969

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.220

Alfa AF: 0.189 Hom.: 2710

Bravo AF: 0.227

Asia WGS AF: 0.154 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.1
Dann	Benign	0.67

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: rs7911748; hg19: chr10-16784810;