rs13379306

chr14-50156098-C-Achr14-50156098-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000555794.2(SOS2):c.*813G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 151,812 control chromosomes in the GnomAD database, including 2,406 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 0.15 (2406 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: SOS2 ENST00000555794.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

SOS2 (HGNC:11188): (SOS Ras/Rho guanine nucleotide exchange factor 2) This gene encodes a regulatory protein that is involved in the positive regulation of ras proteins. Mutations in this gene are associated with Noonan Syndrome-9. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOS2	NM_006939.4	c.2057+901G>T		intron_variant		ENST00000216373.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOS2	ENST00000555794.2	c.*813G>T		3_prime_UTR_variant	6/6	1
SOS2	ENST00000216373.10	c.2057+901G>T		intron_variant		1	NM_006939.4	P1
SOS2	ENST00000543680.5	c.1958+901G>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23437 AN: 151692 Hom.: 2407 Cov.: 31

Gnomad AFR AF: 0.0515

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.179

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.154 AC: 23433 AN: 151812 Hom.: 2406 Cov.: 31 AF XY: 0.158 AC XY: 11716 AN XY: 74170

Gnomad4 AFR AF: 0.0514

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.183

Alfa AF: 0.150 Hom.: 191

Bravo AF: 0.166

Asia WGS AF: 0.208 AC: 722 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.44
Dann	Benign	0.32

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: rs13379306; hg19: chr14-50622816;