10-16701673-A-G

Variant names:

• chr10-16701673-A-G
• rs10795417
• NM_012425.4:c.599-6518T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012425.4(RSU1):​c.599-6518T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,954 control chromosomes in the GnomAD database, including 14,551 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 0.43 (14551 hom., cov: 32)
• Consequence: RSU1 NM_012425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.914
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012425.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSU1	NM_012425.4	MANE Select	c.599-6518T>C		intron	N/A	NP_036557.1
	RSU1	NM_152724.3		c.440-6518T>C		intron	N/A	NP_689937.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSU1	ENST00000345264.10	TSL:1 MANE Select	c.599-6518T>C		intron	N/A	ENSP00000339521.5
	RSU1	ENST00000377921.7	TSL:1	c.599-6518T>C		intron	N/A	ENSP00000367154.3
	RSU1	ENST00000602389.1	TSL:1	c.440-6518T>C		intron	N/A	ENSP00000473588.1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 65982 AN: 151836 Hom.: 14536 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.435 AC: 66032 AN: 151954 Hom.: 14551 Cov.: 32 AF XY: 0.431 AC XY: 31979 AN XY: 74266

African (AFR) AF: 0.507 AC: 20988 AN: 41420

American (AMR) AF: 0.421 AC: 6418 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1675 AN: 3468

East Asian (EAS) AF: 0.476 AC: 2458 AN: 5162

South Asian (SAS) AF: 0.383 AC: 1843 AN: 4816

European-Finnish (FIN) AF: 0.366 AC: 3855 AN: 10544

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27448 AN: 67980

Other (OTH) AF: 0.432 AC: 910 AN: 2108

Alfa AF: 0.418 Hom.: 17035

Bravo AF: 0.443

Asia WGS AF: 0.449 AC: 1559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.32
DANN	Benign	0.48
PhyloP100		-0.91
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10795417; hg19: chr10-16743672;