rs7910261

chr10-16755034-A-G

Variant summary

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

The NM_012425.4(RSU1):c.282-45T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 1,169,496 control chromosomes in the GnomAD database, including 58,928 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 0.42 (17639 hom., cov: 32)
  • Exomes 𝑓: 0.27 (41289 hom.)
• Consequence: RSU1 NM_012425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.851

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSU1	NM_012425.4	c.282-45T>C		intron_variant		ENST00000345264.10
RSU1	NM_152724.3	c.123-45T>C		intron_variant
RSU1	XM_047425617.1	c.282-45T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSU1	ENST00000345264.10	c.282-45T>C		intron_variant		1	NM_012425.4	P1

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63443 AN: 152018 Hom.: 17571 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.405

GnomAD3 exomes AF: 0.298 AC: 69838 AN: 234722 Hom.: 12902 AF XY: 0.287 AC XY: 36459 AN XY: 126898

Gnomad AFR exome AF: 0.807

Gnomad AMR exome AF: 0.224

Gnomad ASJ exome AF: 0.248

Gnomad EAS exome AF: 0.415

Gnomad SAS exome AF: 0.254

Gnomad FIN exome AF: 0.222

Gnomad NFE exome AF: 0.256

Gnomad OTH exome AF: 0.293

GnomAD4 exome AF: 0.267 AC: 271354 AN: 1017360 Hom.: 41289 Cov.: 13 AF XY: 0.264 AC XY: 138644 AN XY: 524410

Gnomad4 AFR exome AF: 0.816

Gnomad4 AMR exome AF: 0.243

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.379

Gnomad4 SAS exome AF: 0.254

Gnomad4 FIN exome AF: 0.224

Gnomad4 NFE exome AF: 0.247

Gnomad4 OTH exome AF: 0.296

GnomAD4 genome AF: 0.418 AC: 63579 AN: 152136 Hom.: 17639 Cov.: 32 AF XY: 0.412 AC XY: 30661 AN XY: 74384

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.410

Alfa AF: 0.320 Hom.: 2255

Bravo AF: 0.445

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.048
Dann	Benign	0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7910261; hg19: chr10-16797033; COSMIC: COSV61716466;