10-16695165-G-GC

Variant names:

• chr10-16695165-G-GC
• rs372430392
• NM_012425.4:c.599-11_599-10insG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_012425.4(RSU1):​c.599-11_599-10insG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000405 in 1,430,888 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 22)
  • Exomes 𝑓: 0.000042 (1 hom.)
• Consequence: RSU1 NM_012425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 0 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: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSU1	NM_012425.4	c.599-11_599-10insG		intron_variant	Intron 7 of 8	ENST00000345264.10	NP_036557.1
RSU1	NM_152724.3	c.440-11_440-10insG		intron_variant	Intron 6 of 7		NP_689937.2
RSU1	XM_047425617.1	c.598+57373_598+57374insG		intron_variant	Intron 6 of 6		XP_047281573.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSU1	ENST00000345264.10	c.599-11_599-10insG		intron_variant	Intron 7 of 8	1	NM_012425.4	ENSP00000339521.5

Frequencies

GnomAD3 genomes AF: 0.0000201 AC: 2 AN: 99578 Hom.: 0 Cov.: 22

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000433

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000646 AC: 10 AN: 154806 AF XY: 0.0000831

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000932

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000421 AC: 56 AN: 1331310 Hom.: 1 Cov.: 26 AF XY: 0.0000392 AC XY: 26 AN XY: 663732

African (AFR) AF: 0.00 AC: 0 AN: 29366

American (AMR) AF: 0.00 AC: 0 AN: 34814

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22966

East Asian (EAS) AF: 0.00142 AC: 51 AN: 35904

South Asian (SAS) AF: 0.00 AC: 0 AN: 78542

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47802

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5196

European-Non Finnish (NFE) AF: 0.00000391 AC: 4 AN: 1022324

Other (OTH) AF: 0.0000184 AC: 1 AN: 54396

GnomAD4 genome AF: 0.0000201 AC: 2 AN: 99578 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 48052

African (AFR) AF: 0.00 AC: 0 AN: 27452

American (AMR) AF: 0.00 AC: 0 AN: 9802

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2132

East Asian (EAS) AF: 0.00 AC: 0 AN: 2942

South Asian (SAS) AF: 0.00 AC: 0 AN: 2854

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6136

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 192

European-Non Finnish (NFE) AF: 0.0000433 AC: 2 AN: 46138

Other (OTH) AF: 0.00 AC: 0 AN: 1324

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.28

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: rs372430392; hg19: chr10-16737164;