10-16811077-A-G

Variant names:

• chr10-16811077-A-G
• rs1797076
• NM_012425.4:c.109+5896T>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.109+5896T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 151,934 control chromosomes in the GnomAD database, including 26,306 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 0.57 (26306 hom., cov: 31)
• Consequence: RSU1 NM_012425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.705
• Publications: 7 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 = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSU1	NM_012425.4	c.109+5896T>C		intron_variant	Intron 2 of 8	ENST00000345264.10	NP_036557.1
RSU1	NM_152724.3	c.-51+6238T>C		intron_variant	Intron 1 of 7		NP_689937.2
RSU1	XM_047425617.1	c.109+5896T>C		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+5896T>C		intron_variant	Intron 2 of 8	1	NM_012425.4	ENSP00000339521.5

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86205 AN: 151816 Hom.: 26268 Cov.: 31

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.568 AC: 86298 AN: 151934 Hom.: 26306 Cov.: 31 AF XY: 0.573 AC XY: 42526 AN XY: 74250

African (AFR) AF: 0.787 AC: 32617 AN: 41440

American (AMR) AF: 0.570 AC: 8703 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1413 AN: 3472

East Asian (EAS) AF: 0.792 AC: 4091 AN: 5168

South Asian (SAS) AF: 0.515 AC: 2478 AN: 4814

European-Finnish (FIN) AF: 0.550 AC: 5786 AN: 10522

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29525 AN: 67934

Other (OTH) AF: 0.531 AC: 1121 AN: 2112

Alfa AF: 0.462 Hom.: 6253

Bravo AF: 0.583

Asia WGS AF: 0.645 AC: 2244 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	5.0
DANN	Benign	0.31
PhyloP100		0.70
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: rs1797076; hg19: chr10-16853076;