chr10-16701366-A-G

Variant names:

• chr10-16701366-A-G
• rs7093729
• NM_012425.4:c.599-6211T>C

Variant summary

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

The NM_012425.4(RSU1):​c.599-6211T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,120 control chromosomes in the GnomAD database, including 44,910 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 0.76 (44910 hom., cov: 32)
• Consequence: RSU1 NM_012425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSU1	NM_012425.4	c.599-6211T>C		intron_variant	Intron 7 of 8	ENST00000345264.10	NP_036557.1
RSU1	NM_152724.3	c.440-6211T>C		intron_variant	Intron 6 of 7		NP_689937.2
RSU1	XM_047425617.1	c.598+51173T>C		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.599-6211T>C		intron_variant	Intron 7 of 8	1	NM_012425.4	ENSP00000339521.5

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115562 AN: 152004 Hom.: 44855 Cov.: 32

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.760 AC: 115667 AN: 152120 Hom.: 44910 Cov.: 32 AF XY: 0.760 AC XY: 56523 AN XY: 74356

African (AFR) AF: 0.916 AC: 38029 AN: 41530

American (AMR) AF: 0.659 AC: 10071 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2762 AN: 3472

East Asian (EAS) AF: 0.893 AC: 4625 AN: 5178

South Asian (SAS) AF: 0.743 AC: 3582 AN: 4822

European-Finnish (FIN) AF: 0.711 AC: 7506 AN: 10554

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.686 AC: 46629 AN: 67970

Other (OTH) AF: 0.736 AC: 1553 AN: 2110

Alfa AF: 0.710 Hom.: 164505

Bravo AF: 0.766

Asia WGS AF: 0.806 AC: 2802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.6
DANN	Benign	0.41
PhyloP100		-0.56
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: rs7093729; hg19: chr10-16743365;