rs7079901

Positions:

• chr10-16698724-A-G
• chr10-16698724-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012425.4(RSU1):​c.599-3569T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,076 control chromosomes in the GnomAD database, including 13,706 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 0.42 (13706 hom., cov: 32)
• Consequence: RSU1 NM_012425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RSU1	NM_012425.4	c.599-3569T>C		intron_variant		ENST00000345264.10
RSU1	NM_152724.3	c.440-3569T>C		intron_variant
RSU1	XM_047425617.1	c.598+53815T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RSU1	ENST00000345264.10	c.599-3569T>C		intron_variant		1	NM_012425.4	P1

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64068 AN: 151958 Hom.: 13688 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.422 AC: 64126 AN: 152076 Hom.: 13706 Cov.: 32 AF XY: 0.418 AC XY: 31107 AN XY: 74370

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.422

Alfa AF: 0.409 Hom.: 1565

Bravo AF: 0.430

Asia WGS AF: 0.391 AC: 1360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.097
DANN	Benign	0.65

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

Publications

LitVar

Other links and lift over

dbSNP: rs7079901; hg19: chr10-16740723;