rs7916663

Variant names:

• chr10-16706611-G-A
• rs7916663
• NM_012425.4:c.599-11456C>T

Variant summary

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

The NM_012425.4(RSU1):​c.599-11456C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 151,976 control chromosomes in the GnomAD database, including 10,340 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 0.29 (10340 hom., cov: 32)
• Consequence: RSU1 NM_012425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.861
• Publications: 6 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSU1	NM_012425.4	c.599-11456C>T		intron_variant	Intron 7 of 8	ENST00000345264.10	NP_036557.1
RSU1	NM_152724.3	c.440-11456C>T		intron_variant	Intron 6 of 7		NP_689937.2
RSU1	XM_047425617.1	c.598+45928C>T		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.599-11456C>T		intron_variant	Intron 7 of 8	1	NM_012425.4	ENSP00000339521.5

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43746 AN: 151858 Hom.: 10325 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.0955

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.288 AC: 43822 AN: 151976 Hom.: 10340 Cov.: 32 AF XY: 0.290 AC XY: 21540 AN XY: 74286

African (AFR) AF: 0.645 AC: 26752 AN: 41448

American (AMR) AF: 0.162 AC: 2480 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0955 AC: 331 AN: 3466

East Asian (EAS) AF: 0.445 AC: 2300 AN: 5170

South Asian (SAS) AF: 0.268 AC: 1288 AN: 4814

European-Finnish (FIN) AF: 0.193 AC: 2040 AN: 10550

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7958 AN: 67960

Other (OTH) AF: 0.224 AC: 471 AN: 2102

Alfa AF: 0.172 Hom.: 11228

Bravo AF: 0.303

Asia WGS AF: 0.367 AC: 1278 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.44
PhyloP100		-0.86
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: rs7916663; hg19: chr10-16748610;