rs1130684

Variant names:

• chr10-16817336-C-A
• rs1130684
• ENST00000377911.1:n.128G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-16817336-C-A
• chr10-16817336-C-G
• chr10-16817336-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000377911.1(RSU1):​n.128G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000065 in 461,784 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 (0 hom., cov: 34)
  • Exomes 𝑓: 0.0000065 (0 hom.)
• Consequence: RSU1 ENST00000377911.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000377911.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSU1	NM_012425.4	MANE Select	c.-25G>T		5_prime_UTR	Exon 1 of 9	NP_036557.1
	RSU1	NM_152724.3		c.-72G>T		5_prime_UTR	Exon 1 of 8	NP_689937.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSU1	ENST00000377911.1	TSL:1	n.128G>T		non_coding_transcript_exon	Exon 1 of 8
	RSU1	ENST00000345264.10	TSL:1 MANE Select	c.-25G>T		5_prime_UTR	Exon 1 of 9	ENSP00000339521.5
	RSU1	ENST00000377921.7	TSL:1	c.-255G>T		5_prime_UTR	Exon 1 of 8	ENSP00000367154.3

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152168 Hom.: 0 Cov.: 34

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000646 AC: 2 AN: 309616 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 162406

African (AFR) AF: 0.00 AC: 0 AN: 9096

American (AMR) AF: 0.00 AC: 0 AN: 11744

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9896

East Asian (EAS) AF: 0.00 AC: 0 AN: 20074

South Asian (SAS) AF: 0.0000625 AC: 2 AN: 32006

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20304

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1368

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 186488

Other (OTH) AF: 0.00 AC: 0 AN: 18640

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152168 Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0 AN XY: 74344

African (AFR) AF: 0.0000241 AC: 1 AN: 41418

American (AMR) AF: 0.00 AC: 0 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5194

South Asian (SAS) AF: 0.00 AC: 0 AN: 4836

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68020

Other (OTH) AF: 0.00 AC: 0 AN: 2094

Alfa AF: 0.00 Hom.: 93

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	7.9
DANN	Benign	0.31
PhyloP100		0.33
PromoterAI		-0.095	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1130684; hg19: chr10-16859335;