rs7087965

Positions:

• chr10-16647684-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSU1	NM_012425.4	c.731+47339C>T		intron_variant		ENST00000345264.10
RSU1	NM_152724.3	c.572+47339C>T		intron_variant
RSU1	XM_047425617.1	c.599-54188C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSU1	ENST00000345264.10	c.731+47339C>T		intron_variant		1	NM_012425.4	P1

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

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.311

Alfa AF: 0.301 Hom.: 9902

Bravo AF: 0.338

Asia WGS AF: 0.309 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.51

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: rs7087965; hg19: chr10-16689683;