10-16592300-C-T

Variant names:

• chr10-16592300-C-T
• rs7068341
• NM_012425.4:c.*1094G>A

Variant summary

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

The NM_012425.4(RSU1):​c.*1094G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,142 control chromosomes in the GnomAD database, including 924 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 0.11 (924 hom., cov: 32)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: RSU1 NM_012425.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 11 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]

ENSG00000287925 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012425.4. 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.*1094G>A		3_prime_UTR	Exon 9 of 9	NP_036557.1
	RSU1	NM_152724.3		c.*1094G>A		3_prime_UTR	Exon 8 of 8	NP_689937.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RSU1	ENST00000345264.10	TSL:1 MANE Select	c.*1094G>A		3_prime_UTR	Exon 9 of 9	ENSP00000339521.5
	RSU1	ENST00000377921.7	TSL:1	c.*1094G>A		3_prime_UTR	Exon 8 of 8	ENSP00000367154.3
	RSU1	ENST00000602389.1	TSL:1	c.*1094G>A		3_prime_UTR	Exon 8 of 8	ENSP00000473588.1

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16892 AN: 152014 Hom.: 923 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0883

Gnomad EAS AF: 0.0967

Gnomad SAS AF: 0.0545

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.124

GnomAD4 exome AF: 0.100 AC: 1 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.111 AC: 16903 AN: 152132 Hom.: 924 Cov.: 32 AF XY: 0.111 AC XY: 8283 AN XY: 74388

African (AFR) AF: 0.110 AC: 4584 AN: 41508

American (AMR) AF: 0.113 AC: 1730 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0883 AC: 306 AN: 3466

East Asian (EAS) AF: 0.0971 AC: 502 AN: 5170

South Asian (SAS) AF: 0.0554 AC: 267 AN: 4822

European-Finnish (FIN) AF: 0.103 AC: 1089 AN: 10586

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8006 AN: 67992

Other (OTH) AF: 0.123 AC: 258 AN: 2102

Alfa AF: 0.114 Hom.: 1876

Bravo AF: 0.112

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.065
DANN	Benign	0.52
PhyloP100		-1.4
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: rs7068341; hg19: chr10-16634299;