chr10-16648572-C-T

Variant names:

• chr10-16648572-C-T
• rs6602141
• NM_012425.4:c.731+46451G>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.731+46451G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 151,894 control chromosomes in the GnomAD database, including 31,055 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 0.63 (31055 hom., cov: 31)
• Consequence: RSU1 NM_012425.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 6 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RSU1	NM_012425.4	c.731+46451G>A		intron_variant	Intron 8 of 8	ENST00000345264.10	NP_036557.1
RSU1	NM_152724.3	c.572+46451G>A		intron_variant	Intron 7 of 7		NP_689937.2
RSU1	XM_047425617.1	c.599-55076G>A		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.731+46451G>A		intron_variant	Intron 8 of 8	1	NM_012425.4	ENSP00000339521.5

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95648 AN: 151776 Hom.: 30992 Cov.: 31

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.631 AC: 95778 AN: 151894 Hom.: 31055 Cov.: 31 AF XY: 0.629 AC XY: 46647 AN XY: 74208

African (AFR) AF: 0.795 AC: 32978 AN: 41466

American (AMR) AF: 0.635 AC: 9686 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1761 AN: 3472

East Asian (EAS) AF: 0.459 AC: 2357 AN: 5134

South Asian (SAS) AF: 0.673 AC: 3238 AN: 4808

European-Finnish (FIN) AF: 0.560 AC: 5885 AN: 10510

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37866 AN: 67938

Other (OTH) AF: 0.617 AC: 1300 AN: 2106

Alfa AF: 0.584 Hom.: 81136

Bravo AF: 0.642

Asia WGS AF: 0.643 AC: 2237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.014
DANN	Benign	0.23
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: rs6602141; hg19: chr10-16690571;