rs780631

chr10-16813930-G-Achr10-16813930-G-T

Variant summary

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

The NM_012425.4(RSU1):c.109+3043C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,208 control chromosomes in the GnomAD database, including 1,860 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 0.14 (1860 hom., cov: 32)
• Consequence: RSU1 NM_012425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSU1	NM_012425.4	c.109+3043C>T		intron_variant		ENST00000345264.10
RSU1	NM_152724.3	c.-51+3385C>T		intron_variant
RSU1	XM_047425617.1	c.109+3043C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSU1	ENST00000345264.10	c.109+3043C>T		intron_variant		1	NM_012425.4	P1

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20733 AN: 152090 Hom.: 1854 Cov.: 32

Gnomad AFR AF: 0.0449

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.136 AC: 20744 AN: 152208 Hom.: 1860 Cov.: 32 AF XY: 0.142 AC XY: 10547 AN XY: 74410

Gnomad4 AFR AF: 0.0448

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.0956

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.117

Alfa AF: 0.152 Hom.: 271

Bravo AF: 0.135

Asia WGS AF: 0.200 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	2.4
Dann	Benign	0.81

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: rs780631; hg19: chr10-16855929;