rs7899853

Variant names:

• chr10-16815604-A-T
• rs7899853
• NM_012425.4:c.109+1369T>A

Variant summary

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

The NM_012425.4(RSU1):​c.109+1369T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,078 control chromosomes in the GnomAD database, including 3,491 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 0.20 (3491 hom., cov: 33)
• Consequence: RSU1 NM_012425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSU1	NM_012425.4	c.109+1369T>A		intron_variant	Intron 2 of 8	ENST00000345264.10	NP_036557.1
RSU1	NM_152724.3	c.-51+1711T>A		intron_variant	Intron 1 of 7		NP_689937.2
RSU1	XM_047425617.1	c.109+1369T>A		intron_variant	Intron 1 of 6		XP_047281573.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RSU1	ENST00000345264.10	c.109+1369T>A		intron_variant	Intron 2 of 8	1	NM_012425.4	ENSP00000339521.5

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30306 AN: 151960 Hom.: 3484 Cov.: 33

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0417

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0957

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.199 AC: 30334 AN: 152078 Hom.: 3491 Cov.: 33 AF XY: 0.193 AC XY: 14346 AN XY: 74362

African (AFR) AF: 0.321 AC: 13297 AN: 41468

American (AMR) AF: 0.149 AC: 2277 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 643 AN: 3462

East Asian (EAS) AF: 0.0420 AC: 218 AN: 5192

South Asian (SAS) AF: 0.144 AC: 695 AN: 4816

European-Finnish (FIN) AF: 0.0957 AC: 1014 AN: 10598

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11620 AN: 67982

Other (OTH) AF: 0.201 AC: 423 AN: 2108

Alfa AF: 0.183 Hom.: 352

Bravo AF: 0.211

Asia WGS AF: 0.0950 AC: 336 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.66
DANN	Benign	0.20
PhyloP100		-0.41
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: rs7899853; hg19: chr10-16857603;