10-16592300-C-T

Position:

• chr10-16592300-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RSU1	NM_012425.4	c.*1094G>A		3_prime_UTR_variant	9/9	ENST00000345264.10	NP_036557.1
RSU1	NM_152724.3	c.*1094G>A		3_prime_UTR_variant	8/8		NP_689937.2
RSU1	XM_047425617.1	c.*961G>A		3_prime_UTR_variant	7/7		XP_047281573.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RSU1	ENST00000345264	c.*1094G>A		3_prime_UTR_variant	9/9	1	NM_012425.4	ENSP00000339521.5
RSU1	ENST00000377921	c.*1094G>A		3_prime_UTR_variant	8/8	1		ENSP00000367154.3
RSU1	ENST00000602389	c.*1094G>A		3_prime_UTR_variant	8/8	1		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

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.00

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

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0883

Gnomad4 EAS AF: 0.0971

Gnomad4 SAS AF: 0.0554

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.123

Alfa AF: 0.115 Hom.: 1361

Bravo AF: 0.112

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.065
DANN	Benign	0.52

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: rs7068341; hg19: chr10-16634299;