10-16809409-C-A

Position:

• chr10-16809409-C-A

Variant summary

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

The NM_012425.4(RSU1):​c.109+7564G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,056 control chromosomes in the GnomAD database, including 1,645 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 0.13 (1645 hom., cov: 32)
• Consequence: RSU1 NM_012425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSU1	NM_012425.4	c.109+7564G>T		intron_variant		ENST00000345264.10
RSU1	NM_152724.3	c.-51+7906G>T		intron_variant
RSU1	XM_047425617.1	c.109+7564G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSU1	ENST00000345264.10	c.109+7564G>T		intron_variant		1	NM_012425.4	P1

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19066 AN: 151938 Hom.: 1639 Cov.: 32

Gnomad AFR AF: 0.0428

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.125 AC: 19082 AN: 152056 Hom.: 1645 Cov.: 32 AF XY: 0.132 AC XY: 9826 AN XY: 74328

Gnomad4 AFR AF: 0.0427

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.106

Alfa AF: 0.123 Hom.: 847

Bravo AF: 0.126

Asia WGS AF: 0.202 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.017
DANN	Benign	0.49

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: rs921742; hg19: chr10-16851408;