12-111446804-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_005475.3(SH2B3):c.784T>C(p.Trp262Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 1,570,508 control chromosomes in the GnomAD database, including 282,793 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.68 (37727 hom., cov: 32)
  • Exomes 𝑓: 0.57 (245066 hom.)
• Consequence: SH2B3 NM_005475.3 missense
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 0.878

Genes affected

SH2B3 (HGNC:29605): (SH2B adaptor protein 3) This gene encodes a member of the SH2B adaptor family of proteins, which are involved in a range of signaling activities by growth factor and cytokine receptors. The encoded protein is a key negative regulator of cytokine signaling and plays a critical role in hematopoiesis. Mutations in this gene have been associated with susceptibility to celiac disease type 13 and susceptibility to insulin-dependent diabetes mellitus. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2014]

ATXN2 (HGNC:10555): (ataxin 2) This gene belongs to a group of genes that is associated with microsatellite-expansion diseases, a class of neurological and neuromuscular disorders caused by expansion of short stretches of repetitive DNA. The protein encoded by this gene has two globular domains near the N-terminus, one of which contains a clathrin-mediated trans-Golgi signal and an endoplasmic reticulum exit signal. The encoded cytoplasmic protein localizes to the endoplasmic reticulum and plasma membrane, is involved in endocytosis, and modulates mTOR signals, modifying ribosomal translation and mitochondrial function. The N-terminal region of the protein contains a polyglutamine tract of 14-31 residues that can be expanded in the pathogenic state to 32-200 residues. Intermediate length expansions of this tract increase susceptibility to amyotrophic lateral sclerosis, while long expansions of this tract result in spinocerebellar ataxia-2, an autosomal-dominantly inherited, neurodegenerative disorder. Genome-wide association studies indicate that loss-of-function mutations in this gene may be associated with susceptibility to type I diabetes, obesity and hypertension. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=1.2047894E-6).
• BP6: Variant 12-111446804-T-C is Benign according to our data. Variant chr12-111446804-T-C is described in ClinVar as [Benign]. Clinvar id is 1265448.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SH2B3	NM_005475.3	c.784T>C	p.Trp262Arg	missense_variant	3/8	ENST00000341259.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SH2B3	ENST00000341259.7	c.784T>C	p.Trp262Arg	missense_variant	3/8	1	NM_005475.3	P1
SH2B3	ENST00000538307.1	c.178T>C	p.Trp60Arg	missense_variant	2/7	2
ATXN2	ENST00000642389.2	c.*171-2617A>G		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102715 AN: 151964 Hom.: 37652 Cov.: 32

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.647

GnomAD3 exomes AF: 0.667 AC: 147137 AN: 220466 Hom.: 53297 AF XY: 0.661 AC XY: 77382 AN XY: 117014

Gnomad AFR exome AF: 0.931

Gnomad AMR exome AF: 0.789

Gnomad ASJ exome AF: 0.341

Gnomad EAS exome AF: 0.999

Gnomad SAS exome AF: 0.898

Gnomad FIN exome AF: 0.603

Gnomad NFE exome AF: 0.511

Gnomad OTH exome AF: 0.601

GnomAD4 exome AF: 0.571 AC: 809276 AN: 1418426 Hom.: 245066 Cov.: 36 AF XY: 0.577 AC XY: 403420 AN XY: 699524

Gnomad4 AFR exome AF: 0.935

Gnomad4 AMR exome AF: 0.774

Gnomad4 ASJ exome AF: 0.349

Gnomad4 EAS exome AF: 0.999

Gnomad4 SAS exome AF: 0.892

Gnomad4 FIN exome AF: 0.599

Gnomad4 NFE exome AF: 0.514

Gnomad4 OTH exome AF: 0.598

GnomAD4 genome AF: 0.676 AC: 102854 AN: 152082 Hom.: 37727 Cov.: 32 AF XY: 0.688 AC XY: 51173 AN XY: 74348

Gnomad4 AFR AF: 0.918

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.905

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.650

Alfa AF: 0.544 Hom.: 52514

Bravo AF: 0.690

TwinsUK AF: 0.509 AC: 1889

ALSPAC AF: 0.550 AC: 2118

ESP6500AA AF: 0.906 AC: 3992

ESP6500EA AF: 0.495 AC: 4254

ExAC AF: 0.662 AC: 79944

Asia WGS AF: 0.943 AC: 3277 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 30, 2023	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 10, 2019	This variant is associated with the following publications: (PMID: 26553438, 28628107, 29547645, 21909115, 26621817, 18311140, 20546165, 23222517, 24777453, 19820697, 19198610, 17554260, 24026423, 24482502, 20560212) -

Primary myelofibrosis;C3277671:Thrombocythemia 1;C4551637:Primary familial polycythemia due to EPO receptor mutation Benign:1

Benign, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

May 16, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.048
BayesDel_addAF	Benign	-0.65	T
BayesDel_noAF	Benign	-0.57
Cadd	Benign	13
Dann	Benign	0.24
DEOGEN2	Benign	0.25	T;.
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.077	N
LIST_S2	Benign	0.0068	T;T
MetaRNN	Benign	0.0000012	T;T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	-2.3	N;.
MutationTaster	Benign	1.0	P;P;P
PrimateAI	Benign	0.33	T
PROVEAN	Benign	4.2	N;N
REVEL	Benign	0.16
Sift	Benign	1.0	T;T
Sift4G	Benign	1.0	T;T
Polyphen		0.0	B;B
Vest4		0.040
MutPred		0.15		Gain of disorder (P = 0.0048);.;
MPC		0.11
ClinPred		0.0019	T
GERP RS		3.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.10
gMVP		0.36

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs3184504; hg19: chr12-111884608; COSMIC: COSV57981059; COSMIC: COSV57981059;