10-16701673-A-G

Position:

• chr10-16701673-A-G

Variant summary

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

The NM_012425.4(RSU1):​c.599-6518T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,954 control chromosomes in the GnomAD database, including 14,551 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 0.43 (14551 hom., cov: 32)
• Consequence: RSU1 NM_012425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.914

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]

RSU1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RSU1	NM_012425.4	c.599-6518T>C		intron_variant		ENST00000345264.10	NP_036557.1
RSU1	NM_152724.3	c.440-6518T>C		intron_variant			NP_689937.2
RSU1	XM_047425617.1	c.598+50866T>C		intron_variant			XP_047281573.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RSU1	ENST00000345264.10	c.599-6518T>C		intron_variant		1	NM_012425.4	ENSP00000339521.5

Frequencies

GnomAD3 genomes AF: 0.435 AC: 65982 AN: 151836 Hom.: 14536 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.435 AC: 66032 AN: 151954 Hom.: 14551 Cov.: 32 AF XY: 0.431 AC XY: 31979 AN XY: 74266

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.432

Alfa AF: 0.413 Hom.: 12581

Bravo AF: 0.443

Asia WGS AF: 0.449 AC: 1559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.32
DANN	Benign	0.48

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: rs10795417; hg19: chr10-16743672;