rs1671308

Variant names:

• chr10-16808537-A-T
• rs1671308
• NM_012425.4:c.109+8436T>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+8436T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 150,334 control chromosomes in the GnomAD database, including 2,139 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 0.15 (2139 hom., cov: 30)
• Consequence: RSU1 NM_012425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSU1	NM_012425.4	c.109+8436T>A		intron_variant	Intron 2 of 8	ENST00000345264.10	NP_036557.1
RSU1	NM_152724.3	c.-51+8778T>A		intron_variant	Intron 1 of 7		NP_689937.2
RSU1	XM_047425617.1	c.109+8436T>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+8436T>A		intron_variant	Intron 2 of 8	1	NM_012425.4	ENSP00000339521.5

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22447 AN: 150264 Hom.: 2133 Cov.: 30

Gnomad AFR AF: 0.0488

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.149 AC: 22463 AN: 150334 Hom.: 2139 Cov.: 30 AF XY: 0.155 AC XY: 11371 AN XY: 73210

African (AFR) AF: 0.0488 AC: 2002 AN: 41042

American (AMR) AF: 0.242 AC: 3640 AN: 15054

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 432 AN: 3458

East Asian (EAS) AF: 0.305 AC: 1532 AN: 5030

South Asian (SAS) AF: 0.186 AC: 885 AN: 4768

European-Finnish (FIN) AF: 0.235 AC: 2344 AN: 9980

Middle Eastern (MID) AF: 0.0448 AC: 13 AN: 290

European-Non Finnish (NFE) AF: 0.166 AC: 11241 AN: 67726

Other (OTH) AF: 0.130 AC: 270 AN: 2082

Alfa AF: 0.168 Hom.: 312

Bravo AF: 0.148

Asia WGS AF: 0.223 AC: 776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.71
PhyloP100		-1.3
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: rs1671308; hg19: chr10-16850536;